1
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Influence of Mutations of Conserved Arginines on Neuropeptide Binding in the DPP III Active Site. Molecules 2023; 28:molecules28041976. [PMID: 36838964 PMCID: PMC9967118 DOI: 10.3390/molecules28041976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
Dipeptidyl peptidase III (DPP III), a zinc exopeptidase, is involved in the final steps of intercellular protein degradation and has a marked affinity for opioid peptides such as enkephalins and endomorphins. Recently, we characterized a number of neuropeptides as potential substrates and inhibitors of human DPP III and provided an explanation for their differential behavior. These studies prompted us to investigate the influence of the conserved R399 and R669 on neuropeptides binding to DPP III. Measuring kinetic parameters in inhibitory assays, we found that mutation of R669 to Ala or Met significantly reduced the inhibitory properties of the slow substrates tynorphin and valorphin, whereas the effects on binding of the good substrates Arg2-2NA and Leu-enkephalin were small. Molecular dynamics simulations of wild-type (WT) and mutant DPP III complexes with Leu-enkephalin, tynorphin, valorphin, and Arg2-2NA in conjunction with calculations of binding free energies revealed that the lower inhibitory potency of slow substrates in the R669A mutant can be explained by the lower binding affinity of tynorphin and the higher propensity of valorphin to hydrolyze in the mutant than in WT. The R399A mutation was shown to affect the binding and/or hydrolysis of both good and slow substrates, with the effects on Leu-enkephalin being the most pronounced.
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2
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Survey of Dipeptidyl Peptidase III Inhibitors: From Small Molecules of Microbial or Synthetic Origin to Aprotinin. Molecules 2022; 27:molecules27093006. [PMID: 35566358 PMCID: PMC9101112 DOI: 10.3390/molecules27093006] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/30/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) was originally thought to be a housekeeping enzyme that contributes to intracellular peptide catabolism. More specific roles for this cytosolic metallopeptidase, in the renin-angiotensin system and oxidative stress regulation, were confirmed, or recognized, only recently. To prove indicated (patho)physiological functions of DPP III in cancer progression, cataract formation and endogenous pain modulation, or to reveal new ones, selective and potent inhibitors are needed. This review encompasses natural and synthetic compounds with experimentally proven inhibitory activity toward mammalian DPP III. Except for the polypeptide aprotinin, all others are small molecules and include flavonoids, coumarin and benzimidazole derivatives. Presented are current strategies for the discovery or development of DPP III inhibitors, and mechanisms of inhibitory actions. The most potent inhibitors yet reported (propioxatin A and B, Tyr-Phe- and Phe-Phe-NHOH, and JMV-390) are active in low nanomolar range and contain hydroxamic acid moiety. High inhibitory potential possesses oligopeptides from the hemorphin group, valorphin and tynorphin, which are poor substrates of DPP III. The crystal structure of human DPP III-tynorphin complex enabled the design of the transition-state peptidomimetics inhibitors, effective in low micromolar concentrations. A new direction in the field is the development of fluorescent inhibitor for monitoring DPP III activity.
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3
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Ivkovic J, Jha S, Lembacher-Fadum C, Puschnig J, Kumar P, Reithofer V, Gruber K, Macheroux P, Breinbauer R. Efficient Entropy-Driven Inhibition of Dipeptidyl Peptidase III by Hydroxyethylene Transition-State Peptidomimetics. Chemistry 2021; 27:14108-14120. [PMID: 34314529 PMCID: PMC8518066 DOI: 10.1002/chem.202102204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Indexed: 12/30/2022]
Abstract
Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed Zn‐dependent protease, which plays an important role in regulating endogenous peptide hormones, such as enkephalins or angiotensins. In previous biophysical studies, it could be shown that substrate binding is driven by a large entropic contribution due to the release of water molecules from the closing binding cleft. Here, the design, synthesis and biophysical characterization of peptidomimetic inhibitors is reported, using for the first time an hydroxyethylene transition‐state mimetic for a metalloprotease. Efficient routes for the synthesis of both stereoisomers of the pseudopeptide core were developed, which allowed the synthesis of peptidomimetic inhibitors mimicking the VVYPW‐motif of tynorphin. The best inhibitors inhibit DPP3 in the low μM range. Biophysical characterization by means of ITC measurement and X‐ray crystallography confirm the unusual entropy‐driven mode of binding. Stability assays demonstrated the desired stability of these inhibitors, which efficiently inhibited DPP3 in mouse brain homogenate.
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Affiliation(s)
- Jakov Ivkovic
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | | | - Johannes Puschnig
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
| | - Prashant Kumar
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, 8010, Graz, Austria
| | - Viktoria Reithofer
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, 8010, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstr. 50, 8010, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010, Graz, Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010, Graz, Austria
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4
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Agić D, Brkić H, Kazazić S, Tomić A, Abramić M. Aprotinin interacts with substrate-binding site of human dipeptidyl peptidase III. J Biomol Struct Dyn 2019; 37:3596-3606. [DOI: 10.1080/07391102.2018.1521343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Dejan Agić
- Department of Chemistry, Faculty of Agriculture in Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Hrvoje Brkić
- Department of Biophysics and Radiology, Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
- Department of Biophysics and Radiology, Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Saša Kazazić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonija Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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5
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Tomić A, Kovačević B, Tomić S. Concerted nitrogen inversion and hydrogen bonding to Glu451 are responsible for protein-controlled suppression of the reverse reaction in human DPP III. Phys Chem Chem Phys 2018; 18:27245-27256. [PMID: 27711538 DOI: 10.1039/c6cp04580d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Human dipeptidyl-peptidase III (h.DPP III) is a zinc-exopeptidase that hydrolyses dipeptides from the N-terminus of its substrates. Its mechanism of action was assumed to be similar to that of thermolysin, but was never thoroughly investigated. This study presents the first insight into the reaction mechanism of h.DPP III, determined on the model and real (hydrated enzyme with Leu-enkephalin bound in the active site) systems. The Glu451-assisted water addition on amide carbon atoms and nitrogen inversion (i.e. change of pyramidalization on the leaving nitrogen) are shown to be the rate-determining steps with the activation energies in a good agreement with the experimental results for the Leu-enkephalin hydrolysis. The energy barrier for nucleophilic attack is about 28 kJ mol-1, while barriers for the N-inversion differ as a consequence of the number of hydrogen bonds that have to be changed, which is smaller in the model active site than in the solvated enzyme. Although precisely defined geometry of the enzyme binding site puts an additional restraint on the hydrogen bonding interactions, at the same time it stimulates the forward reaction towards the final hydrolytic product. Namely, different from the model, the N-inversion is in a concerted fashion followed by favourable hydrogen bonding with Glu451 that immediately "locks" the system into the configuration where reversion to the enzyme-substrate complex is hardly achievable. Therefore we propose that the functional significance of DPP III is dual: to lower the energy barrier of the peptide hydrolysis and to suppress the reverse reaction.
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Affiliation(s)
- A Tomić
- Department of Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000, Zagreb, Croatia.
| | - B Kovačević
- Department of Physical Chemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000, Zagreb, Croatia.
| | - S Tomić
- Department of Organic Chemistry and Biochemistry, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000, Zagreb, Croatia.
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6
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Prajapati SC, Singh R, Chauhan SS. Human dipeptidyl peptidase III regulates G-protein coupled receptor-dependent Ca2+ concentration in human embryonic kidney 293T cells. Biol Chem 2017; 397:563-9. [PMID: 26887037 DOI: 10.1515/hsz-2016-0117] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/15/2016] [Indexed: 01/08/2023]
Abstract
The precise biological function of human dipeptidyl peptidase III (hDPP III) is poorly understood. Using luciferase reporter constructs responsive to change in Ca2+ and/or cAMP and Fura 2-AM fluorometric assay, we show a significant decrease in intracellular Ca2+ following hDPP III overexpression and angiotensin II stimulation in angiotensin II type 1 receptor (G-protein coupled receptor, GPCR) expressing HEK293T cells. Silencing the expression of hDPP III by siRNA reversed the effect of hDPP III overexpression with a concomitant increase in Ca2+. These results, for the first time, show involvement of hDPP III in GPCR dependent Ca2+ regulation in HEK293T cells.
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7
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Lu K, Alcivar AL, Ma J, Foo TK, Zywea S, Mahdi A, Huo Y, Kensler TW, Gatza ML, Xia B. NRF2 Induction Supporting Breast Cancer Cell Survival Is Enabled by Oxidative Stress-Induced DPP3-KEAP1 Interaction. Cancer Res 2017; 77:2881-2892. [PMID: 28416489 DOI: 10.1158/0008-5472.can-16-2204] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 02/17/2017] [Accepted: 03/31/2017] [Indexed: 01/11/2023]
Abstract
NRF2 is a transcription factor serving as a master regulator of the expression of many genes involved in cellular responses to oxidative and other stresses. In the absence of stress, NRF2 is constantly synthesized but maintained at low levels as it is targeted by KEAP1 for ubiquitination and proteasome-mediated degradation. NRF2 binds KEAP1 mainly through a conserved "ETGE" motif that has also been found in several other proteins, such as DPP3, which has been shown to bind KEAP1 and enhance NRF2 function upon overexpression. Here we demonstrate the interaction between endogenous DPP3 and endogenous KEAP1. We further show that the DPP3-KEAP1 interaction is strongly induced by hydrogen peroxide and that DPP3 is required for timely NRF2 induction and nuclear accumulation in the estrogen receptor (ER)-positive MCF7 breast cancer cells. Moreover, we present evidence that the binding of DPP3 to KEAP1 stabilizes the latter. Finally, we show that DPP3 is overexpressed in breast cancer and that elevated levels of DPP3 mRNA correlate with increased NRF2 downstream gene expression and poor prognosis, particularly for ER-positive breast cancer. Our studies reveal novel insights into the regulation of NRF2 and identify DPP3 and an NRF2 transcriptional signature as potential biomarkers for breast cancer prognosis and treatment. Cancer Res; 77(11); 2881-92. ©2017 AACR.
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Affiliation(s)
- Kevin Lu
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Allen L Alcivar
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Jianglin Ma
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Tzeh Keong Foo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Susan Zywea
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Amar Mahdi
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Yanying Huo
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Thomas W Kensler
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Michael L Gatza
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey
| | - Bing Xia
- Department of Radiation Oncology, Rutgers Cancer Institute of New Jersey and Robert Wood Johnson Medical School, New Brunswick, New Jersey.
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8
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Karačić Z, Vukelić B, Ho GH, Jozić I, Sučec I, Salopek-Sondi B, Kozlović M, Brenner SE, Ludwig-Müller J, Abramić M. A novel plant enzyme with dual activity: an atypical Nudix hydrolase and a dipeptidyl peptidase III. Biol Chem 2017; 398:101-112. [PMID: 27467751 PMCID: PMC5606203 DOI: 10.1515/hsz-2016-0141] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 07/25/2016] [Indexed: 11/15/2022]
Abstract
In a search for plant homologues of dipeptidyl peptidase III (DPP III) family, we found a predicted protein from the moss Physcomitrella patens (UniProt entry: A9TLP4), which shared 61% sequence identity with the Arabidopsis thaliana uncharacterized protein, designated Nudix hydrolase 3. Both proteins contained all conserved regions of the DPP III family, but instead of the characteristic hexapeptide HEXXGH zinc-binding motif, they possessed a pentapeptide HEXXH, and at the N-terminus, a Nudix box, a hallmark of Nudix hydrolases, known to act upon a variety of nucleoside diphosphate derivatives. To investigate their biochemical properties, we expressed heterologously and purified Physcomitrella (PpND) and Arabidopsis (AtND) protein. Both hydrolyzed, with comparable catalytic efficiency, the isopentenyl diphosphate (IPP), a universal precursor for the biosynthesis of isoprenoid compounds. In addition, PpND dephosphorylated four purine nucleotides (ADP, dGDP, dGTP, and 8-oxo-dATP) with strong preference for oxidized dATP. Furthermore, PpND and AtND showed DPP III activity against dipeptidyl-2-arylamide substrates, which they cleaved with different specificity. This is the first report of a dual activity enzyme, highly conserved in land plants, which catalyzes the hydrolysis of a peptide bond and of a phosphate bond, acting both as a dipeptidyl peptidase III and an atypical Nudix hydrolase.
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Affiliation(s)
- Zrinka Karačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Bojana Vukelić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Gabrielle H. Ho
- Department of Plant & Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720, USA
| | - Iva Jozić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Iva Sučec
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Branka Salopek-Sondi
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Marija Kozlović
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
| | - Steven E. Brenner
- Department of Plant & Microbial Biology, University of California, 461 Koshland Hall, Berkeley, CA 94720, USA
| | - Jutta Ludwig-Müller
- Institut für Botanik, Technische Universität Dresden, Zellescher Weg 20b, 01062 Dresden Germany
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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9
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Matovina M, Agić D, Abramić M, Matić S, Karačić Z, Tomić S. New findings about human dipeptidyl peptidase III based on mutations found in cancer. RSC Adv 2017. [DOI: 10.1039/c7ra02642k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work we investigated the role of two highly conserved residues in the peptidase family M49, whose mutations G313W and R510W were detected in human cancer, using combined experimental and computational approaches.
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Affiliation(s)
- M. Matovina
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - D. Agić
- Josip Juraj Strossmayer University of Osijek
- Faculty of Agriculture in Osijek
- Osijek
- Croatia
| | - M. Abramić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - S. Matić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - Z. Karačić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - S. Tomić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
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10
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Tomin M, Tomić S. Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study. MOLECULAR BIOSYSTEMS 2017; 13:2407-2417. [PMID: 28971197 DOI: 10.1039/c7mb00310b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Dynamics and enzyme activity of dipeptidyl peptidase III, wild type and mutants, from the human gut symbiont Bacteroides thetaiotaomicron.
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Affiliation(s)
- M. Tomin
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
| | - S. Tomić
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
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11
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Cvitešić A, Sabljić I, Makarević J, Abramić M. Novel dipeptidyl hydroxamic acids that inhibit human and bacterial dipeptidyl peptidase III. J Enzyme Inhib Med Chem 2016; 31:40-45. [PMID: 27226411 DOI: 10.1080/14756366.2016.1186021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Human dipeptidyl peptidase III (hDPP III), a zinc-metallopeptidase of the family M49, is an activator of the Keap1-Nrf2 cytoprotective pathway involved in defense against oxidative stress. Pathophysiological roles of DPP III have not been elucidated yet, partly due to the lack of specific inhibitors. We showed that substrate analog H-Tyr-Phe-NHOH is a strong competitive inhibitor of hDPP III, while H-Tyr-Gly-NHOH expresses much weaker inhibition. To investigate the effects of amino acid substitutions in inhibitor P1 position, we synthesized three new dipeptidyl hydroxamates and examined their influence on the activity of hDPP III and DPP III from the human gut symbiont Bacteroides thetaiotaomicron. The extent of inhibition of hDPP III, but not of bacterial enzyme, was dependent on the amino acid in P1. H-Phe-Phe-NHOH is recognized as one of the strongest inhibitors of hDPP III (Ki = 0.028 μM), and H-Phe-Leu-NHOH discriminated between human and bacterial ortholog of the M49 family.
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Affiliation(s)
- Ana Cvitešić
- a Division of Organic Chemistry and Biochemistry , and
| | - Igor Sabljić
- b Division of Physical Chemistry , Ruđer Bošković Institute , Bijenička cesta 54 , Zagreb , Croatia
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12
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Hast BE, Goldfarb D, Mulvaney KM, Hast MA, Siesser PF, Yan F, Hayes DN, Major MB. Proteomic analysis of ubiquitin ligase KEAP1 reveals associated proteins that inhibit NRF2 ubiquitination. Cancer Res 2013; 73:2199-210. [PMID: 23382044 PMCID: PMC3618590 DOI: 10.1158/0008-5472.can-12-4400] [Citation(s) in RCA: 198] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Somatic mutations in the KEAP1 ubiquitin ligase or its substrate NRF2 (NFE2L2) commonly occur in human cancer, resulting in constitutive NRF2-mediated transcription of cytoprotective genes. However, many tumors display high NRF2 activity in the absence of mutation, supporting the hypothesis that alternative mechanisms of pathway activation exist. Previously, we and others discovered that via a competitive binding mechanism, the proteins WTX (AMER1), PALB2, and SQSTM1 bind KEAP1 to activate NRF2. Proteomic analysis of the KEAP1 protein interaction network revealed a significant enrichment of associated proteins containing an ETGE amino acid motif, which matches the KEAP1 interaction motif found in NRF2. Like WTX, PALB2, and SQSTM1, we found that the dipeptidyl peptidase 3 (DPP3) protein binds KEAP1 via an "ETGE" motif to displace NRF2, thus inhibiting NRF2 ubiquitination and driving NRF2-dependent transcription. Comparing the spectrum of KEAP1-interacting proteins with the genomic profile of 178 squamous cell lung carcinomas characterized by The Cancer Genome Atlas revealed amplification and mRNA overexpression of the DPP3 gene in tumors with high NRF2 activity but lacking NRF2 stabilizing mutations. We further show that tumor-derived mutations in KEAP1 are hypomorphic with respect to NRF2 inhibition and that DPP3 overexpression in the presence of these mutants further promotes NRF2 activation. Collectively, our findings further support the competition model of NRF2 activation and suggest that "ETGE"-containing proteins such as DPP3 contribute to NRF2 activity in cancer.
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MESH Headings
- Adaptor Proteins, Signal Transducing/physiology
- Animals
- Apoptosis
- Blotting, Western
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Cell Proliferation
- Cells, Cultured
- Cohort Studies
- Cytoskeletal Proteins/physiology
- Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/genetics
- Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/metabolism
- Embryo, Mammalian/cytology
- Embryo, Mammalian/metabolism
- Fibroblasts/cytology
- Fibroblasts/metabolism
- Humans
- Immunoenzyme Techniques
- Kelch-Like ECH-Associated Protein 1
- Kidney/cytology
- Kidney/metabolism
- Luciferases/metabolism
- Lung/metabolism
- Lung/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/metabolism
- Lung Neoplasms/pathology
- Mice
- Mice, Knockout
- Mutagenesis, Site-Directed
- Mutation/genetics
- NF-E2-Related Factor 2/metabolism
- Proteomics
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Reverse Transcriptase Polymerase Chain Reaction
- Ubiquitin/metabolism
- Ubiquitination
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Affiliation(s)
- Bridgid E. Hast
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
| | - Dennis Goldfarb
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Box#3175, Chapel Hill, NC 27599, USA
| | - Kathleen M. Mulvaney
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
| | - Michael A. Hast
- Department of Biochemistry, Duke University Medical Center, Box #3711, Durham NC, 27710, USA
| | - Priscila F. Siesser
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
| | - Feng Yan
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
| | - D. Neil Hayes
- Department of Internal Medicine and Otolaryngology, Division of Medical Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
| | - Michael B. Major
- Department of Cell Biology and Physiology, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Box#7295, Chapel Hill, NC 27599, USA
- Department of Computer Science, University of North Carolina at Chapel Hill, Box#3175, Chapel Hill, NC 27599, USA
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13
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Vukelić B, Salopek-Sondi B, Špoljarić J, Sabljić I, Meštrović N, Agić D, Abramić M. Reactive cysteine in the active-site motif of Bacteroides thetaiotaomicron dipeptidyl peptidase III is a regulatory residue for enzyme activity. Biol Chem 2013; 393:37-46. [PMID: 22628297 DOI: 10.1515/bc-2011-193] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 11/17/2011] [Indexed: 11/15/2022]
Abstract
Dipeptidyl peptidase III (DPP III), a member of the metallopeptidase family M49, was considered as an exclusively eukaryotic enzyme involved in intracellular peptide catabolism and pain modulation. In 2003, new data on genome sequences revealed the first prokaryotic orthologs, which showed low sequence similarity to eukaryotic ones and a cysteine (Cys) residue in the zinc-binding motif HEXXGH. Here we report the cloning and heterologous expression of DPP III from the human gut symbiont Bacteroides thetaiotaomicron. The catalytic efficiency of bacterial DPP III for preferred synthetic substrate hydrolysis was very similar to that of the human host enzyme. Substitution of Cys450 from the active-site motif by serine did not substantially change the enzymatic activity. However, this residue was wholly responsible for the inactivation effect of sulfhydryl reagents. Molecular modeling indicated seven basic amino acid residues in the local environment of Cys450 as a possible cause for its high reactivity. Sequence analysis of 81 bacterial M49 peptidases showed conservation of the HECLGH motif in 68 primary structures with the majority of proteins lacking an active-site Cys originated from aerobic bacteria. Data obtained suggest that Cys450 of B. thetaiotaomicron DPP III is a regulatory residue for the enzyme activity.
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Affiliation(s)
- Bojana Vukelić
- Division of Organic Chemistry and Biochemistry, Rudjer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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14
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Hirose J, Hata T, Kawaoka C, Ikeura T, Kitahara S, Horii K, Tomida H, Iwamoto H, Ono Y, Fukasawa KM. Flexibility of the coordination geometry around the cupric ions in Cu(II)-rat dipeptidyl peptidase III is important for the expression of enzyme activity. Arch Biochem Biophys 2012; 525:71-81. [DOI: 10.1016/j.abb.2012.05.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Revised: 05/26/2012] [Accepted: 05/28/2012] [Indexed: 11/29/2022]
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15
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Tomić A, González M, Tomić S. The large scale conformational change of the human DPP III-substrate prefers the "closed" form. J Chem Inf Model 2012; 52:1583-94. [PMID: 22656863 DOI: 10.1021/ci300141k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human dipeptidyl peptidase III (DPP III) is a two domain metallo-peptidase from the M49 family. The wide interdomain cleft and broad substrate specificity suggest that this enzyme could experience significant conformational change. Long (>100 ns) molecular dynamics (MD) simulations of DPP III revealed large range conformational changes of the protein, suggesting the pre-existing equilibrium model for a substrate binding. The binding free energy calculations revealed tighter binding of the preferred synthetic substrate Arg-Arg-2-naphtylamide to the "closed" than to the "open" DPP III conformation. Our assumption that Asp372 plays a crucial role in the large scale interdomain closure was proved by the MD simulations of the Asp372Ala variant. During the same simulation time, the variant remained more "open" than the wild type protein. Apparently, Ala was not as efficient as Asp in establishing the interdomain interactions. According to the MM-PBSA calculations, the electrostatic component of the free energy of solvation turned out to be higher for the "closed" protein than for its less compact form. However, the gain in entropy due to water released from the interdomain cleft nicely balanced this negative effect.
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Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia
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16
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Entropy-driven binding of opioid peptides induces a large domain motion in human dipeptidyl peptidase III. Proc Natl Acad Sci U S A 2012; 109:6525-30. [PMID: 22493238 DOI: 10.1073/pnas.1118005109] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Opioid peptides are involved in various essential physiological processes, most notably nociception. Dipeptidyl peptidase III (DPP III) is one of the most important enkephalin-degrading enzymes associated with the mammalian pain modulatory system. Here we describe the X-ray structures of human DPP III and its complex with the opioid peptide tynorphin, which rationalize the enzyme's substrate specificity and reveal an exceptionally large domain motion upon ligand binding. Microcalorimetric analyses point at an entropy-dominated process, with the release of water molecules from the binding cleft ("entropy reservoir") as the major thermodynamic driving force. Our results provide the basis for the design of specific inhibitors that enable the elucidation of the exact role of DPP III and the exploration of its potential as a target of pain intervention strategies.
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17
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Spoljarić J, Salopek-Sondi B, Makarević J, Vukelić B, Agić D, Simaga S, Jajcanin-Jozić N, Abramić M. Absolutely conserved tryptophan in M49 family of peptidases contributes to catalysis and binding of competitive inhibitors. Bioorg Chem 2009; 37:70-6. [PMID: 19375145 DOI: 10.1016/j.bioorg.2009.03.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2008] [Revised: 03/10/2009] [Accepted: 03/11/2009] [Indexed: 11/27/2022]
Abstract
The role of the unique fully conserved tryptophan in metallopeptidase family M49 (dipeptidyl peptidase III family) was investigated by site-directed mutagenesis on human dipeptidyl peptidase III (DPP III) where Trp300 was subjected to two substitutions (W300F and W300L). The mutant enzymes showed thermal stability equal to the wild-type DPP III. Conservative substitution of the Trp300 with phenylalanine decreased enzyme activity 2-4 fold, but did not significantly change the K(m) values for two dipeptidyl 2-naphthylamide substrates. However, the K(m) for the W300L mutant was elevated 5-fold and the k(cat) value was reduced 16-fold with Arg-Arg-2-naphthylamide. Both substitutions had a negative effect on the binding of two competitive inhibitors designed to interact with S1 and S2 subsites. These results indicate the importance of the aromatic nature of W300 in DPP III ligand binding and catalysis, and contribution of this residue in maintaining the functional integrity of this enzyme's S2 subsite.
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Affiliation(s)
- Jasminka Spoljarić
- Division of Organic Chemistry and Biochemistry, Ruder Bosković Institute, Bijenicka cesta 54, P.O. Box 180, HR-10002 Zagreb, Croatia
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18
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Bruce LA, Sigman JA, Randall D, Rodriguez S, Song MM, Dai Y, Elmore DE, Pabon A, Glucksman MJ, Wolfson AJ. Hydrogen bond residue positioning in the 599-611 loop of thimet oligopeptidase is required for substrate selection. FEBS J 2008; 275:5607-17. [PMID: 18959747 DOI: 10.1111/j.1742-4658.2008.06685.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Thimet oligopeptidase (EC 3.4.24.15) is a zinc(II) endopeptidase implicated in the processing of numerous physiological peptides. Although its role in selecting and processing peptides is not fully understood, it is believed that flexible loop regions lining the substrate-binding site allow the enzyme to conform to substrates of varying structure. This study describes mutant forms of thimet oligopeptidase in which Gly or Tyr residues in the 599-611 loop region were replaced, individually and in combination, to elucidate the mechanism of substrate selection by this enzyme. Decreases in k(cat) observed on mutation of Tyr605 and Tyr612 demonstrate that these residues contribute to the efficient cleavage of most substrates. Modeling studies showing that a hinge-bend movement brings both Tyr612 and Tyr605 within hydrogen bond distance of the cleaved peptide bond supports this role. Thus, molecular modeling studies support a key role in transition state stabilization of this enzyme by Tyr605. Interestingly, kinetic parameters show that a bradykinin derivative is processed distinctly from the other substrates tested, suggesting that an alternative catalytic mechanism may be employed for this particular substrate. The data demonstrate that neither Tyr605 nor Tyr612 is necessary for the hydrolysis of this substrate. Relative to other substrates, the bradykinin derivative is also unaffected by Gly mutations in the loop. This distinction suggests that the role of Gly residues in the loop is to properly orientate these Tyr residues in order to accommodate varying substrate structures. This also opens up the possibility that certain substrates may be cleaved by an open form of the enzyme.
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Affiliation(s)
- Lisa A Bruce
- Chemistry Department, Wellesley College, MA 02481-8203, USA
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