Design and synthesis of dipeptidyl nitriles as potent, selective, and reversible inhibitors of cathepsin C

Guay, Daniel; Beaulieu, Christian; Reddy, T. Jagadeeswar; Zamboni, Robert; Méthot, Nathalie; Rubin, Joel; Ethier, Diane; Percival, M. David

doi:10.1016/j.bmcl.2009.07.114

Cited by 39 publications

(32 citation statements)

References 26 publications

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“…Specifically, we needed to avoid inhibition of the FPs or DPAP3 since these are also essential papain-fold cysteine proteases. Ala-4(I)Phe-DMK (Figure 1A) was initially developed by Merck as an irreversible inhibitor of hCat C (Guay et al, 2009; Methot et al, 2007). The diazomethyl ketone (DMK) reactive group, which selectively targets cysteine proteases (Powers et al, 2002), covalently modifies the catalytic active site cysteine of hCat C. In order to assess the specificity of Ala-4(I)Phe-DMK for DPAP1, DPAP3, and the FPs, we performed competition assays using several activity-based probes (ABPs).…”

Section: Resultsmentioning

confidence: 99%

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Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes

Deu

Leyva

Albrow

et al. 2010

Chemistry & Biology

100

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SUMMARY The widespread resistance of malaria parasites to all affordable drugs has made the identification of new targets urgent. Dipeptidyl aminopeptidases (DPAPs) represent potentially valuable new targets that are involved in hemoglobin degradation (DPAP1) and parasite egress (DPAP3). Here we use activity-based probes to demonstrate that specific inhibition of DPAP1 by a small molecule results in the formation of an immature trophozoite that leads to parasite death. Using computational methods we designed stable, non-peptidic covalent inhibitors that kill Plasmodium falciparum at low nanomolar concentrations. These compounds show signs of slowing parasite growth in a murine model of malaria, which suggests that DPAP1 might be a viable anti-malarial target. Interestingly, we found that re-synthesis and activation of DPAP1 after inhibition is rapid, suggesting that effective drugs would need to sustain DPAP1 inhibition for a period of 2–3h.

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Section: Resultsmentioning

confidence: 99%

“…Ala-4(I)Phe-DMK was a valuable gift from David Percival (Merck); its synthesis and characterization was described in (Guay et al, 2009). The vinyl sulfone inhibitors used in this study were described in (Arastu-Kapur et al, 2008), and KB16 was characterized in (Brak et al, 2008).…”

Section: Methodsmentioning

confidence: 99%

Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes

Deu

Leyva

Albrow

et al. 2010

Chemistry & Biology

100

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“…However, in immune cells it is responsible for activating various granule serine proteases involved in the immune response and inflammation such as neutrophil elastase, chymase, granzyme A and B, or cathepsin G(McGuire et al 1993;Kummer et al 1996;Pham & Ley 1999;Adkison et al 2002). Because of its role in activating pro-inflammatory proteases, CatC has been pursued as a potential target for chronic inflammatory diseases (Guay et al 2009;Lainé et al 2011;Furber et al 2014), and phase I clinical trials with CatC inhibitors have been performed by GSK (GSK2793660) (Miller et al 2017) and Astrazeneca (AZD7986) (Palmér et al 2018), thus proving that DPAPs can be targeted with small drug-like molecules.…”

Section: Introductionmentioning

confidence: 99%

Characterization ofP. falciparumdipeptidyl aminopeptidase 3 specificity reveals structural factors responsible for differences in amino acid preferences between peptide-based substrates and covalent inhibitors

Vries

Groborz

et al. 2018

Preprint

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Dipeptidyl aminopeptidases (DPAPs) are druggable cysteine proteases that cleave dipeptides from the N-terminus of proteins and oligopeptides. Plasmodium DPAPs have been shown to be important for the asexual replication of the malaria parasite and are therefore potential antimalarial targets. DPAP1 seems to be important for parasite growth within infected red blood cells, and DPAP3 plays a critical role in the invasion of erythrocytes by the malaria parasite. An inhibitor able to block both of these proteases will target the parasite at different developmental stages thus making the emergence of drug resistance more difficult.Understanding the substrate specificity of these proteases is important to understand their molecular functions and to help develop potent and selective inhibitors. In this study, we used peptide-based libraries of substrates and inhibitors to determine the specificity of DPAP3 and compared it to that of DPAP1 and human cathepsin C (mammalian DPAP homologue). We then used the structure activity relationships information from these screens to develop optimal DPAP3 fluorogenic substrates as well as highly specific DPAP1 and DPAP3 inhibitors.Interestingly, while the substrate specificity of a protease is often used to develop potent inhibitors, in this study we show that equally potent and highly specific inhibitors can be developed based on the structure of poor substrates. Overall, this study illustrates that focusing the development of peptidic inhibitors solely on the substrate specificity of a protease might overlook important structural features that can be exploited to developed highly potent and selective compounds.not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/246124 doi: bioRxiv preprint first posted online Jan. 11, 2018; 3 Malaria is a devastating infectious parasitic disease causing close to half a million deaths every year 1 . Over the last 15 years the world has seen a very significant drop in malaria incidence, mainly due to the global distribution of insecticide-impregnated bed nets and the use of artemisinin-based combination therapies as the standard of care for uncomplicated malaria 2 .However, malaria remains a major global health burden with half of the world population at risk and around 200 million clinical cases per year. Unfortunately, mosquitoes are becoming increasingly resistance to insecticides 3 and artemisinin resistance is on the rise 4 , thus making the identification of antimalarial targets and the development of drugs with novel mechanisms of action extremely urgent 5 .Malaria is caused by parasites of the Plasmodium genus and is transmitted by Anopheles mosquitoes during a blood meal. Upon infection, malaria parasites first establish an asymptomatic infection in the liver before reaching the blood stream where they replicate asexually through multiple rounds of red blood cell (RBC) invasion, intracellular growth and divis...

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“…[21,22] Bondebjerg et al have extended this strategy for inhibitor design. [21,22] Bondebjerg et al have extended this strategy for inhibitor design.…”

Section: Introductionmentioning

confidence: 99%

“…Most of the cathepsin C inhibitors investigated so far are mimics of dipeptide substrates functionalized with an electrophilic moiety addressing the catalytic residue Cys 234 either in a reversible or irreversible fashion. [21,22] Bondebjerg et al have extended this strategy for inhibitor design. [23] Thus, based on a semicarbazide scaffold, the authors developed inhibitors that allow for addressing the S1' and S2' binding pockets in addition to the S sites in a substrate-like fashion.…”

Section: Introductionmentioning

confidence: 99%

E‐64c‐Hydrazide: A Lead Structure for the Development of Irreversible Cathepsin C Inhibitors

et al. 2013

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Cathepsin C is a papain-like cysteine protease with dipeptidyl aminopeptidase activity that is thought to activate various granule-associated serine proteases. Its exopeptidase activity is structurally explained by the so-called exclusion domain, which blocks the active-site cleft beyond the S2 site and, with its Asp 1 residue, provides an anchoring point for the N terminus of peptide and protein substrates. Here, the hydrazide of (2S,3S)-trans-epoxysuccinyl-L-leucylamido-3-methylbutane (E-64c) (k2/Ki =140±5 M(-1) s(-1)) is demonstrated to be a lead structure for the development of irreversible cathepsin C inhibitors. The distal amino group of the hydrazide moiety addresses the acidic Asp 1 residue at the entrance of the S2 pocket by hydrogen bonding while also occupying the flat hydrophobic S1'-S2' area with its leucine-isoamylamide moiety. Furthermore, structure-activity relationship studies revealed that functionalization of this distal amino group with alkyl residues can be used to occupy the conserved hydrophobic S2 pocket. In particular, the n-butyl derivative was identified as the most potent inhibitor of the series (k2/Ki =56 000±1700 M(-1) s(-1)).

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Design and synthesis of dipeptidyl nitriles as potent, selective, and reversible inhibitors of cathepsin C

Cited by 39 publications

References 26 publications

Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes

Functional Studies of Plasmodium falciparum Dipeptidyl Aminopeptidase I Using Small Molecule Inhibitors and Active Site Probes

Characterization ofP. falciparumdipeptidyl aminopeptidase 3 specificity reveals structural factors responsible for differences in amino acid preferences between peptide-based substrates and covalent inhibitors

E‐64c‐Hydrazide: A Lead Structure for the Development of Irreversible Cathepsin C Inhibitors

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