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Cited by 2Protease and Inhibitor MechanismsNeutrophil, Myeloperoxidase and Oxidative MechanismsRedox biology and oxidative stress

Discrimination of Methionine Sulfoxide and Sulfone by Human Neutrophil Elastase

Open access
Leahy, Darren, Grant, Cameron, Jackson, Alex, Duff, Alex, Tardiota, Nicholas, Van Haeften, Jessica, Chen, Xingchen, Peake, Jonathan M. +5 more·2021·Molecules
DOI 10.3390/molecules26175344PMC PMC8434204
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Abstract

Human neutrophil elastase (HNE) is a uniquely destructive serine protease with the ability to unleash a wave of proteolytic activity by destroying the inhibitors of other proteases. Although this phenomenon forms an important part of the innate immune response to invading pathogens, it is responsible for the collateral host tissue damage observed in chronic conditions such as chronic obstructive pulmonary disease (COPD), and in more acute disorders such as the lung injuries associated with COVID-19 infection. Previously, a combinatorially selected activity-based probe revealed an unexpected substrate preference for oxidised methionine, which suggests a link to oxidative pathogen clearance by neutrophils. Here we use oxidised model substrates and inhibitors to confirm this observation and to show that neutrophil elastase is specifically selective for the di-oxygenated methionine sulfone rather than the mono-oxygenated methionine sulfoxide. We also posit a critical role for ordered solvent in the mechanism of HNE discrimination between the two oxidised forms methionine residue. Preference for the sulfone form of oxidised methionine is especially significant. While both host and pathogens have the ability to reduce methionine sulfoxide back to methionine, a biological pathway to reduce methionine sulfone is not known. Taken together, these data suggest that the oxidative activity of neutrophils may create rapidly cleaved elastase “super substrates” that directly damage tissue, while initiating a cycle of neutrophil oxidation that increases elastase tissue damage and further neutrophil recruitment.

AI snapshot

Written from the paper’s full text.

TL;DR

Human neutrophil elastase (HNE) was found to discriminate between oxidized forms of a P3 methionine residue, strongly preferring methionine sulfone over methionine sulfoxide in peptide substrates and inhibitors. The authors propose that ordered solvent and the HNE S3 pocket explain this selectivity and link it to neutrophil oxidative damage.

Key findings

HNE strongly preferred P3 methionine sulfone: 19 of the 20 highest catalytic rates in a 144-substrate tetrapeptide pNA library contained P3 methionine sulfone, while P2 methionine sulfone and P2 glycine substrates were universally poor. The aldehyde inhibitor Ac-RM(O2)AV-H inhibited HNE with a Ki of 147 nM and showed a 49.4-fold inhibition enhancement relative to non-oxidized Ac-RMAV-H, whereas the sulfoxide derivative Ac-RM(O)AV-H enhanced inhibition only 1.3-fold. N-terminal acetylation had little effect on kcat but reduced KM by approximately one-half; MeOSuc-AAPV-pNA had KM 0.152 mM versus a previously published 0.14 mM. P1 alanine substrates showed at least 3.5-fold higher kcat than P1 valine substrates, but kcat/Km showed no clear distinction.

Methods

A non-combinatorial sparse matrix library of 144 tetrapeptide pNA substrates composed of naturally occurring amino acids was synthesized and screened with HNE purified from purulent human sputum, measuring catalytic rates spectrophotometrically at 405 nm. Selected substrates and peptide aldehyde inhibitors were characterized by Michaelis–Menten kinetics and Morrison tight-binding inhibition analysis. Molecular dynamics simulations were performed using crystal structure 4WVP, explicit TIP3P solvent, CHARMM27, and NAMD/VMD to model RMAV-H, RM(O)AV-H, and RM(O2)AV-H complexes with HNE.

Limitations

Stated: the biological relevance of P3 methionine sulfone remains to be demonstrated in biologically relevant protein molecules, and methionine oxidation to sulfone is infrequent and depends on strong oxidative stress and vulnerable methionine residues. Stated: pNA substrates containing non-oxidized methionine could not be synthesized because pNA incorporation required oxidation during synthesis. Evident: the study uses in vitro peptide substrates, inhibitors, and molecular dynamics predictions, with no cellular or in vivo validation of the proposed oxidative “super substrate” cycle.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.3390/molecules26175344

Cites

45 of 45 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

23 of 37 cited sources checked · 11 supported · 1 flagged · accuracy not yet measured

  • Premisecitation

    SLPI and elafin potencies are diminished, though not completely abolished, under oxidative conditions due to methionine residues in their protease binding loops.

    “Although not completely abolished, the potencies of SLPI and elafin are diminished under oxidative conditions, due to the similar presence of methionine residues in their protease binding loops [16,17].”
    Quote in the paperSubstantial claim1 of 2 sources checked
    • cites [16] Boudier, 1994, Oxidized mucus proteinase inhibitor: A fairly potent neutrophil elastase inhibitor, Biochem. J. source

      The paper identifies mucus proteinase inhibitor (MPI) as SLPI and reports in the Discussion (page unavailable) that oxidation of Met-73 in its inhibitory-site loop diminishes anti-elastase activity without abolishing it. The cited paper does not address elafin, so it does not support extending that finding or its proposed mechanism to elafin. (LLM, conf=0.88)

      Experimental — accuracy not yet measured
    • cites [17] Nobar, 2005, Oxidized elafin and trappin poorly inhibit the elastolytic activity of neutrophil elastase and proteinase 3, FEBS J. source
  • Premisecitation

    The effect of methionine oxidation on HNE cleavage of peptide substrates has a strong positional dependence.

    “However, the oxidation of P3 methionine residues in peptide substrates appears to enhance the HNE catalysed cleavage rates of those substrates [20] and suggests a strong positional dependence.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Kasperkiewicz, 2014, Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling, Proc. Natl. Acad. Sci. USA source

      The Results report that HNE favors methionine dioxide at P3 and recognizes methionine oxide about fivefold less strongly, supporting an effect of oxidation state on substrate recognition. The cited text does not compare oxidized with unoxidized methionine at P3 or directly establish how methionine oxidation affects cleavage at different positions, so the claimed enhancement and strong positional dependence are not fully supported. (LLM, conf=0.78)

      Experimental — accuracy not yet measured
  • Premisecitation

    Crystallography of the PK101-HNE complex revealed an essential hydrogen bond between a sulfonyl oxygen of the oxidised methionine residue and the backbone amide of a unique Gly-Gly motif in the HNE S3 pocket.

    “Subsequent crystallography to characterise the interaction between the screen-selected activity-based probe PK101 and the HNE binding surface revealed an essential hydrogen bond between a sulfonyl oxygen of the oxidised methionine residue and the backbone amide of a unique Gly-Gly motif in the HNE S3 pocket [21].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [21] Lechtenberg, 2015, The Elastase-PK101 Structure: Mechanism of an Ultrasensitive Activity-based Probe Revealed, ACS Chem. Biol. source
  • Premisecitation

    The crystal structure of the methionine sulfonyl-containing inhibitor PK-101 identified a hydrogen bond between its oxidised methionine residue and the main chain amide at Gly219 in the S3 pocket of HNE.

    “The crystal structure of the methionine sulfonyl-containing inhibitor PK-101 [21] identified a hydrogen bond between the oxidised methionine residue present in PK-101 and the main chain amide at Gly219 in the S3 pocket of HNE.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [21] Lechtenberg, 2015, The Elastase-PK101 Structure: Mechanism of an Ultrasensitive Activity-based Probe Revealed, ACS Chem. Biol. source
  • Findingown data

    Overall selectivity of individually synthesised tetrapeptide pNA substrates roughly follows the HNE consensus cleavage sequence in the MEROPS database.

    “Overall, selectivity for these individually synthesised peptides roughly follows the HNE consensus cleavage sequence found in the MEROPS database [28] shown in Figure 1B.”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [28] Rawlings, 2018, The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database, Nucleic Acids Res. source

      The Introduction (page unavailable) says MEROPS contains known cleavage sites for proteins, peptides and synthetic substrates, supporting its use as a source of cleavage data. Our copy does not give an HNE consensus sequence or compare it with the citing authors’ tetrapeptide results, so the specific agreement claimed cannot be verified from this paper. (LLM, conf=0.79)

      Experimental — accuracy not yet measured
  • Classified as probably not a substantial claim. 13
  • May combine two claims. 9

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Inhibitor drugs targeting HNE are small non-proteinaceous synthetic molecules.

    “However, PK101 and the optimal HNE peptide substrates selected from the combinatorial library contain unnatural amino acid residues [20], and the inhibitor drugs targeting HNE are small non-proteinaceous synthetic molecules [22,23].”
    Quote in the paperNot a substantial claim1 of 2 sources checked
    • cites [22] Kawabata, 1991, ONO-5046, a novel inhibitor of human neutrophil elastase, Biochem. Biophys. Res. Commun. source
    • cites [23] Li, 2015, Freezing the Bioactive Conformation to Boost Potency: The Identification of BAY 85-8501, a Selective and Potent Inhibitor of Human Neutrophil Elastase for Pulmonary Diseases, ChemMedChem source

      The Introduction (Figure 2 caption) says that biologicals such as elafin were the first class of HNE-inhibiting drugs, and describes small-molecule drugs as another class. Thus the paper contradicts the unqualified claim that HNE inhibitor drugs are small non-proteinaceous synthetic molecules. (LLM, conf=0.88)

      Checked by a reasoning model — may be wrong.

      Experimental — accuracy not yet measured

  • Classified as probably not a substantial claim.

    Premisecitation

    Oxidation of P3 methionine residues in peptide substrates enhances HNE-catalysed cleavage rates.

    “However, the oxidation of P3 methionine residues in peptide substrates appears to enhance the HNE catalysed cleavage rates of those substrates [20] and suggests a strong positional dependence.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Kasperkiewicz, 2014, Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling, Proc. Natl. Acad. Sci. USA source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    HNE is a causal factor in the progression of emphysema and chronic obstructive pulmonary disease (COPD).

    “However, HNE is also a causal factor in the progression of emphysema and chronic obstructive pulmonary disease (COPD) [6,7] due to the enzyme’s propensity to propagate cyclic inflammation, recruit neutrophils, and proteolytically destroy elastic lung tissue [8,9].”
    Quote in the paperNot a substantial claim2 of 4 sources checked
    • cites [6] Stockley, 1999, Neutrophils and Protease/Antiprotease Imbalance, Am. J. Respir. Crit. Care Med. source
    • cites [7] Tetley, 1993, New perspectives on basic mechanisms in lung disease. 6. Proteinase imbalance: Its role in lung disease, Thorax source

      The emphysema discussion proposes neutrophil elastase (NE, also called HNE) as a key contributor to tissue damage, and the airways-disease discussion links NE activity to chronic obstructive airways disease. But the Summary says prospective human studies are needed to establish a causal relationship between NE and lung disease. The source therefore does not establish HNE as a causal factor in the progression of emphysema and COPD. (LLM, conf=0.89)

      Experimental — accuracy not yet measured
    • cites [8] Snider, 1984, Emphysema and bronchial secretory cell metaplasia induced in hamsters by human neutrophil products, Am. Rev. Respir. Dis. source
    • cites [9] Sandhaus, 2013, Neutrophil Elastase-Mediated Lung Disease, COPD J. Chronic Obstr. Pulm. Dis. source

      In Historical perspectives (page unavailable), the paper calls HNE a potent emphysema-promoting agent in animal studies and assigns it a prominent pathogenic role in COPD associated with alpha-1 antitrypsin deficiency. Augmentation therapy (page unavailable) describes slowing lung-function decline by protecting lung tissue from proteolytic attack. The claim extends that causal role to COPD generally, whereas the paper says cigarette-smoke-induced lung disease involves additional proteases and pathways. (LLM, conf=0.83)

      Experimental — accuracy not yet measured

  • May combine two claims.

    Premisecitation

    The previous combinatorial library [20] was constructed of pools of many thousands of peptides, each in very low concentration, and each individual substrate concentration was likely far below its respective Km.

    “The previous combinatorial library [20] was constructed of pools of many thousands of peptides, each in very low concentration, and each individual substrate concentration was likely to be far below its respective Km.”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Kasperkiewicz, 2014, Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling, Proc. Natl. Acad. Sci. USA source

      The Results describe a combinatorial library screened as peptide mixtures at 50 μM total concentration, supporting the point that individual peptides were present at low concentration. But each well contained 361 peptides, not many thousands, and the paper does not establish that each peptide’s concentration was far below its respective Km. (LLM, conf=0.86)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    HNE has a pronounced preference for peptide substrates with valine at P1, as previously reported.

    “A pronounced HNE preference for peptide substrates with valine at P1 was previously reported [20].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [20] Kasperkiewicz, 2014, Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling, Proc. Natl. Acad. Sci. USA source

  • May combine two claims.

    Premisecitation

    PK101 and the optimal HNE peptide substrates selected from the combinatorial library contain unnatural amino acid residues.

    “However, PK101 and the optimal HNE peptide substrates selected from the combinatorial library contain unnatural amino acid residues [20], and the inhibitor drugs targeting HNE are small non-proteinaceous synthetic molecules [22,23].”
    Quote in the paperSubstantial claim1 of 1 sources checked
    • cites [20] Kasperkiewicz, 2014, Design of ultrasensitive probes for human neutrophil elastase through hybrid combinatorial substrate library profiling, Proc. Natl. Acad. Sci. USA source

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Oxidation of methionine is a two-step process, in which the methionine residue is first oxidised to the sulfoxide and then irreversibly oxidised to the sulfone.

    “Oxidation of methionine is a two-step process, in which the methionine residue is first oxidised to the sulfoxide and then irreversibly oxidised to the sulfone [30].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [30] Hoshi, 2001, Regulation of cell function by methionine oxidation and reduction, J. Physiol. source

      The passage labeled Abstract (page unavailable) describes oxidation of methionine to methionine sulfoxide, followed by further oxidation to methionine sulfone in the presence of a strong oxidant. It does not say that the second step is irreversible, and the claim omits the strong-oxidant condition. (LLM, conf=0.84)

      Experimental — accuracy not yet measured

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Oxidised methionine residues have been observed in biological samples.

    “Although unusual, oxidised methionine residues have been observed in biological samples [32].”
    Quote in the paperNot a substantial claim1 of 1 sources checked
    • cites [32] Kim, 2014, Methionine oxidation and reduction in proteins, Biochim. Biophys. Acta Gen. Subj. source

  • May combine two claims.

    Findingown data

    Human neutrophil elastase is specifically selective for the di-oxygenated methionine sulfone over the mono-oxygenated methionine sulfoxide, as shown with oxidised model substrates and inhibitors.

    “Here we use oxidised model substrates and inhibitors to confirm this observation and to show that neutrophil elastase is specifically selective for the di-oxygenated methionine sulfone rather than the mono-oxygenated methionine sulfoxide.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    HNE selectivity for methionine sulfone is position dependent; methionine sulfone at P2 makes universally poor substrates.

    “This selectivity was position dependent, as peptides containing methionine sulfone in the P2 position made universally poor substrates.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    Molecular dynamics model predicts that the side chain of P3 methionine and P3 methionine sulfoxide residues deflect away from the active site, while the P3 methionine sulfone residue side chain inserts into the shallow HNE S3 pocket aided by a partial occupancy (20%) hydrogen bond between the second sulfonyl oxygen and the main chain of Gly193.

    “The model predicts that the side chain of the P3 methionine and P3 methionine sulfoxide residues will deflect away from the active site, whilst the P3 methionine sulfone residue side chain will insert into the shallow HNE S3 pocket aided by a partial occupancy (20%) hydrogen bond between the second sulfonyl oxygen and the main chain of Gly193.”
    Quote in the paperSubstantial claim

  • May combine two claims.

    Findingown data

    N-terminal acetylation of the best tetrapeptide substrates increased substrate binding affinity to HNE without appreciably affecting the catalysis mechanism in the active site.

    “N-terminal acetylation increased substrate binding affinity to HNE without appreciably affecting the catalysis mechanism in the active site.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Findingown data

    HNE exhibits strong selectivity for methionine sulfone residues at position P3, with such substrates accounting for 19 of the 20 highest observed catalytic rates.

    “These data confirm a strong selectivity for methionine sulfone residues at position P3, as peptide substrates that included a methionine sulfone residue at position P3 exhibited 19 of the 20 highest observed rates.”
    • Also stated in: § 3.1. Tetrapeptide Substrates Composed of Naturally Occurring Amino Acids Containing a P3 Methionine Sulfone Residue Enhance HNE Catalysis · plain
      “The highest HNE catalysed rates were observed for peptide substrates from our library containing a P3 methionine sulfone residue.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationnone given

    Ordered solvent plays a critical role in the mechanism by which HNE discriminates between the two oxidised forms of methionine.

    “We also posit a critical role for ordered solvent in the mechanism of HNE discrimination between the two oxidised forms methionine residue.”
    Quote in the paperNot a substantial claim

  • May combine two claims.

    Premisecitation

    HNE is targeted by reversible inhibitors including SLPI and elafin, and by the irreversible serpin A1AT, which predominately controls HNE activity in the lung.

    “To ameliorate the hazards of unrestrained HNE activity, the enzyme is targeted by reversible inhibitors, including the secretory leukoprotease inhibitor (SLPI) [11], elafin [12], and the irreversible serpin inhibitor alpha 1 anti-trypsin (A1AT), which predominately controls HNE activity in the lung.”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [11] Rice, 1990, Regulation of proteolysis at the neutrophil-substrate interface by secretory leukoprotease inhibitor, Science source
    • cites [12] Wiedow, 1990, Elafin: An elastase-specific inhibitor of human skin. Purification, characterization, and complete amino acid sequence, J. Biol. Chem. source

  • May combine two claims.

    Interpretationown data

    For P1 valine substrates, strong substrate affinity offset weak catalysis in the binding site; for P1 alanine substrates, poor binding affinity was offset by strong catalysis.

    “With respect to P1 valine efficiency, strong substrate affinity offset weak catalysis in the binding site, while with respect to P1 alanine efficiency, poor binding affinity was offset by strong catalysis.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductown data

    Substrate library kinetic assays were performed in triplicate.

    “reactions were initiated by addition of HNE purified from purulent human sputum (Elastin Products Company, Owensville, MO, USA) to triplicate microplate wells containing each substrate”
    Quote in the paperNot a substantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    Each HNE/inhibitor complex was subjected to three independent molecular dynamics production runs.

    “Each of the three complexes were subject to molecular dynamics consisting of a three-step relaxation followed by three independent production runs of 10 ns simulation time [43].”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Study design and conductown data

    Synthesized peptides were validated by LC-MS after purification.

    “Post purification, peptide containing fractions were analysed by LC-MS on a Sciex QTrap 4500 Q1 scan over 50–1500 m/z.”
    Quote in the paperSubstantial claim

  • Classified as probably not a substantial claim.

    Study design and conductnone given

    HNE active site concentration was determined by titration with A1AT before in-depth kinetic assays.

    “For in-depth assays of candidate substrates and inhibitors, the active site concentration of HNE was first determined by titration with A1AT.”
    Quote in the paperSubstantial claim

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Collateral damage from HNE may also occur in acute conditions such as COVID-19 lung damage.

    “Such collateral damage may also be occurring in acute conditions such as the lung damage caused by COVID-19 infection.”
    Quote in the paperNot a substantial claim

  • Classified as probably not a substantial claim.

    Interpretationreasoning

    The biological relevance of P3 methionine sulfone remains to be demonstrated in biologically relevant protein molecules.

    “but this remains to be demonstrated in biologically relevant protein molecules.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Methionine oxidation to the sulfone is infrequent.
    • Rests on an assumption: Methionine oxidation to the sulfone depends on a combination of strong oxidative stress and the intrinsic vulnerability of only select methionine residues.
22 of 22

  • The paper relies on this without support.

    No biological pathway is known to reduce methionine sulfone.

    “While both host and pathogens have the ability to reduce methionine sulfoxide back to methionine, a biological pathway to reduce methionine sulfone is not known.”

  • The paper relies on this without support.

    Both host and pathogens can reduce methionine sulfoxide back to methionine.

    “While both host and pathogens have the ability to reduce methionine sulfoxide back to methionine, a biological pathway to reduce methionine sulfone is not known.”

  • The paper relies on this without support.

    Peptide aldehyde inhibitors bind at serine protease active sites similarly to their cognate substrates.

    “Since these inhibitors bind at serine protease active sites similarly to their cognate substrates”

  • The paper relies on this without support.

    In vitro HNE substrate selectivity data can be extrapolated to in vivo targeting of naturally occurring substrates under neutrophil-induced oxidative conditions.

    “As our library contained only peptide substrates comprised of genomically encoded amino acids, this suggests that HNE can specifically target naturally occurring substrates in vivo under neutrophil-induced oxidative conditions.”

  • The paper relies on this without support.

    Biologically relevant substrate cleavage sites are embedded in the interior of longer protein chains and rarely near the positively charged N-terminus.

    “Finally, unlike the tetrapeptide substrates used in the sparse matrix library, biologically relevant substrate cleavage sites are embedded in the interior of longer protein chains, and therefore rarely near the positively charged N-terminus.”

  • The paper relies on this without support.

    The diglycine motif associated with the S3 pocket is unique to HNE among all human serine proteases and is a hallmark of an adaptation to oxidised substrates.

    “The associated diglycine motif is unique to HNE among all human serine proteases and is a hallmark of an adaptation to oxidised substrates.”

  • The paper relies on this without support.

    Aldehyde HNE inhibitors suggest that the P3 methionine sulfone residue increases binding affinity.

    “As our aldehyde HNE inhibitors suggest that the P3 methionine sulfone residue increases binding affinity, decreasing the Km would explain why a P3 methionine sulfone enhances HNE catalysis while a P3 methionine sulfoxide does not.”

  • The paper relies on this without support.

    The sulfoxide moiety is a substrate for repair enzymes that are vital for bacterial resistance to neutrophil killing.

    “The sulfoxide moiety is a substrate for repair enzymes that are vital for bacterial resistance to neutrophil killing.”

  • The paper relies on this without support.

    Methionine sulfoxide reductase A and B convert partially oxidised methionine back to the reduced form.

    “These enzymes, methionine sulfoxide reductase A and B, convert partially oxidised methionine back to the reduced form.”

  • The paper relies on this without support.

    The methionine sulfone residue contains two sulfonyl oxygens.

    “In contrast, the methionine sulfone residue contains two sulfonyl oxygens, and is predicted to simultaneously form hydrogen bonds with both the solvent water molecule and the main chain amide at Gly219 (see Figure S1 for trajectories).”

  • The paper relies on this without support.

    Methionine oxidation to the sulfone is infrequent.

    “However, methionine oxidation to the sulfone is infrequent”

  • The paper relies on this without support.

    Methionine oxidation to the sulfone depends on a combination of strong oxidative stress and the intrinsic vulnerability of only select methionine residues.

    “depends on a combination of strong oxidative stress and the intrinsic vulnerability of only select methionine residues.”

  • The paper relies on this without support.

    Endogenous oxidation systems can inactivate HNE's chief inhibitor.

    “the demonstrated ability of endogenous oxidation systems to inactivate HNE’s chief inhibitor”
13 of 13

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Conflicting molecular-dynamics production run lengths

    Major

    The methods describe the same three independent production runs as lasting both 10 ns and 20 ns each.

  • Conflicting glycine residues named for the sulfone hydrogen bond

    Minor

    The results identify Gly193 as the backbone partner for the P3 methionine sulfone hydrogen bond, while the discussion identifies Gly219 for that interaction.

2 of 2

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Authors
Leahy, D., Grant, C., Jackson, A., Duff, A., Tardiota, N., Van Haeften, J., Chen, X., Peake, J. M., Kruppa, M. D., Smith, E. T., Johnson, D. A., Lott, W. B., & Harris, J. M.
Affiliations
  • Queensland University of Technology (AU)
  • School of Biomedical Science, Faculty of Health, Queensland University of Technology, Brisbane, QLD 4059, Australia
  • Chinese Academy of Sciences (CN)
  • East Tennessee State University (US)
  • Stanford Medicine (US)
Corresponding author
Harris, Jonathan M.
ORCID
Venue
Molecules
Publisher
MDPI AG
Published
2021-09-02
Volume
26
Issue
17
Pages
5344
ISSN
1420-3049 (ISSN-L)
DOI
10.3390/molecules26175344
PMC
PMC8434204
OpenAlex
W3196450431
Semantic Scholar
a58ea37aac809256abe867c4ac30e5c05e8e8af9
Cited by
2
References
44
Citations by year
2025: 1 · 2024: 1
FWCI
0.08
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecules (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • QUT ePrints (Queensland University of Technology) (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by)
  • Digital Commons - East Tennessee State University (East Tennessee State University) (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Protease and Inhibitor Mechanisms
  • Life Sciences › Immunology and Microbiology › Immunology › Neutrophil, Myeloperoxidase and Oxidative Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Redox biology and oxidative stress
Keywords
human neutrophil elastase, methionine sulfoxide, methionine sulfone, oxidized methionine, substrate specificity, serine protease, activity-based probes, neutrophil respiratory burst, host tissue damage, chronic obstructive pulmonary disease, protease inhibitors
MeSH terms
COVID-19, SARS-CoV-2, Humans, Immunity, Innate, Lung, Methionine, Neutrophils, Oxidation-Reduction, Substrate Specificity, Leukocyte Elastase, Catalytic Domain, Neutrophil Infiltration, Pulmonary Disease, Chronic Obstructive, Host-Pathogen Interactions, Biocatalysis, Molecular Dynamics Simulation, Enzyme Assays, Proteolysis

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