Peptidyl α-Ketoamides with Nucleobases, Methylpiperazine, and Dimethylaminoalkyl Substituents as Calpain Inhibitors

Ovat, Asli; Li, Zhao Zhao; Hampton, Christina Y.; Asress, Seneshaw; Fernández, Facundo M.; Glass, Jonathan D.; Powers, James C.

doi:10.1021/jm901221v

Cited by 31 publications

(15 citation statements)

References 87 publications

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“…13–20 The problems with this approach are twofold: 1) the papain super-family has a highly conserved active site cleft, which complicates identification of peptidomimetic side chains that differentially bind to individual enzymes, and 2) small peptides do not bind well to calpains.…”

Section: Introductionmentioning

confidence: 99%

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

et al. 2012

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We have designed a highly specific inhibitor of calpain by mimicking a natural protein-protein interaction between calpain and its endogenous inhibitor calpastatin. To enable this goal we established a new method of stabilizing an α-helix in a small peptide by screening twenty-four commercially available crosslinkers for successful cysteine alkylation in a model peptide sequence. The effects of crosslinking on the α-helicity of selected peptides were examined by CD and NMR spectroscopy, and revealed structurally rigid crosslinkers to be the best at stabilizing α-helices. We applied this strategy to the design of inhibitors of calpain that are based on calpastatin, an intrinsically unstable polypeptide that becomes structured upon binding to the enzyme. A two-turn α-helix that binds proximal to the active site cleft was stabilized, resulting in a potent and selective inhibitor for calpain. We further expanded the utility of this inhibitor by developing irreversible calpain family activity-based probes (ABPs), which retained the specificity of the stabilized helical inhibitor. We believe the inhibitor and ABPs and will be useful for future investigation of calpains, while the crosslinking technique will enable exploration of other protein-protein interactions.

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Section: Introductionmentioning

confidence: 99%

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

et al. 2012

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“…Calpain has been implicated in the proteolysis of the Na+/Ca+ exchanger resulting in a reduced expulsion of the Ca++ ions resulting in an ion imbalance that favors a Ca+ influx resulting in the activation of Ca++-dependent calpain [22]. Aberrant activation of this enzyme promotes the breakdown of kinases, phosphatases, transcription factors and the proteolysis of cytoskeletal proteins all of which contribute to neuronal cell death [3]. Thus, using calpain-inhibitors can prevent many processes involved in neuronal cell homeostasis, integrity, plasticity and repair.…”

Section: Discussionmentioning

confidence: 99%

“…Calpains belong to a family of calcium-dependant cysteine proteases of which there are at least 14 different members [3]. Aberrant activation of this enzyme promotes the breakdown of kinases, phosphatases, transcription factors and the proteolysis of cytoskeletal proteins includingalpha-spectrin, all of which contribute to neuronal cell death [4].…”

Section: Introductionmentioning

confidence: 99%

A novel calpain inhibitor for treatment of transient retinal ischemia in the rat

David

Melamud²,

Kesner³

et al. 2011

NeuroReport

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Following an acute ischemia/reperfusion of the rat retina, the activation of cytotoxic proteases, including calpain, results in necrosis and apoptosis of retinal ganglion cells resulting in their degeneration. Using a systemically administered calpain inhibitor that crosses the Blood-Retinal-Barrier would provide for novel systemic intervention that protects the retina from acute injury and lost function. Here we study a novel calpain peptide inhibitor, cysteic–leucyl–argininal (CYLA), in an in vivo rat model of retinal ischemia to determine functional protection using electroretinography. The CYLA-prodrug was administered intraperitoneally before and/or after ischemia-reperfusion at concentrations of 20-40 mg/kg. We found that administering 20 mg/kg CYLA even only after ischemia provides significant preservation of retinal function.

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“…The advantage of the α-ketoamides is that their warhead can interact with the catalytic center of the target proteases by two hydrogen-bonding interactions, namely, via the α-keto oxygen and amide oxygen [ 1 ]. Whereas, warheads like aldehydes or Michael acceptors interacts with the catalytic center by only one hydrogen bond, the α-ketoamide motif is emerging as the most promising group with a possible reversible inhibition of the enzyme's activity better than the other investigated C-terminus warheads [ 23 , 24 ] The α-keto group of the α-ketoamide forms a reversible tetrahedral adduct with the active cysteine enzyme. For example, calpain I inhibitors form tetrahedral hemiketal adduct by the cysteine residue (Cys 115 ) onto the α-keto group of the α-ketoamide [ 25 ].…”

Section: Introductionmentioning

confidence: 99%

An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study

Banerjee¹

2021

Biophysical Chemistry

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The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (M pro ) is an attractive target for anti-coronavirus drug design. Further, α-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of α-ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM = quantum mechanical, SQM = semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys 145 SγH) and simultaneous reversible nucleophilic attack of sulfur onto the α-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys 145 SγH to His 41 Nδ forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the α-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl group plays an important role. Moreover, as the α-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM and pure DFT method. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader's Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis

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Peptidyl α-Ketoamides with Nucleobases, Methylpiperazine, and Dimethylaminoalkyl Substituents as Calpain Inhibitors

Cited by 31 publications

References 87 publications

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

Development of α-Helical Calpain Probes by Mimicking a Natural Protein–Protein Interaction

A novel calpain inhibitor for treatment of transient retinal ischemia in the rat

An insight into the interaction between α-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study

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