1
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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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2
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Malovan G, Hierzberger B, Suraci S, Schaefer M, Santos K, Jha S, Macheroux P. The emerging role of dipeptidyl peptidase 3 in pathophysiology. FEBS J 2022; 290:2246-2262. [PMID: 35278345 DOI: 10.1111/febs.16429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/25/2022] [Accepted: 03/10/2022] [Indexed: 12/17/2022]
Abstract
Dipeptidyl peptidase 3 (DPP3), a zinc-dependent aminopeptidase, is a highly conserved enzyme among higher animals. The enzyme cleaves dipeptides from the N-terminus of tetra- to decapeptides, thereby taking part in activation as well as degradation of signalling peptides critical in physiological and pathological processes such as blood pressure regulation, nociception, inflammation and cancer. Besides its catalytic activity, DPP3 moonlights as a regulator of the cellular oxidative stress response pathway, e.g., the Keap1-Nrf2 mediated antioxidative response. The enzyme is also recognized as a key modulator of the renin-angiotensin system. Recently, DPP3 has been attracting growing attention within the scientific community, which has significantly augmented our knowledge of its physiological relevance. Herein, we review recent advances in our understanding of the structure and catalytic activity of DPP3, with a focus on attributing its molecular architecture and catalytic mechanism to its wide-ranging biological functions. We further highlight recent intriguing reports that implicate a broader role for DPP3 as a valuable biomarker in cardiovascular and renal pathologies and furthermore discuss its potential as a promising drug target.
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Affiliation(s)
- Grazia Malovan
- Institute of Biochemistry, Graz University of Technology, Austria
| | | | - Samuele Suraci
- Department of Experimental and Clinical Medicine, University of Florence, Italy
| | - Maximilian Schaefer
- Institute of Pharmacy, Freie Universität Berlin, Germany.,4TEEN4 Pharmaceuticals GmbH, Hennigsdorf, Germany.,Department of Biology, ETH Zurich, Switzerland
| | | | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Austria
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3
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Interdisciplinary Study of the Effects of Dipeptidyl-Peptidase III Cancer Mutations on the KEAP1-NRF2 Signaling Pathway. Int J Mol Sci 2022; 23:ijms23041994. [PMID: 35216111 PMCID: PMC8878202 DOI: 10.3390/ijms23041994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/02/2022] [Accepted: 02/08/2022] [Indexed: 12/17/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) is associated with cancer progression via interaction with KEAP1, leading to upregulation of the KEAP1-NRF2 oxidative stress pathway. Numerous DPP III mutations have been found in human tumor genomes, and it is suggested that some of them may alter affinity for KEAP1. One such example is the DPP III-R623W variant, which in our previous study showed much higher affinity for the Kelch domain of KEAP1 than the wild-type protein. In this work, we have investigated the effects of this mutation in cultured cells and the effects of several other DPP III mutations on the stability of KEAP1-DPP III complex using an interdisciplinary approach combining biochemical, biophysical and molecular biology methods with computational studies. We determined the affinity of the DPP III variants for the Kelch domain experimentally and by molecular modeling, as well as the effects of the R623W on the expression of several NRF2-controlled genes. We confirmed that the R623W variant upregulates NQO1 expression at the transcriptional level. This supports the hypothesis from our previous study that the increased affinity of the R623W variant for KEAP1 leads to upregulation of the KEAP1-NRF2 pathway. These results provide a new perspective on the involvement of DPP III in cancer progression and prognosis.
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4
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Ban Ž, Karačić Z, Tomić S, Amini H, Marder TB, Piantanida I. Triarylborane Dyes as a Novel Non-Covalent and Non-Inhibitive Fluorimetric Markers for DPP III Enzyme. Molecules 2021; 26:molecules26164816. [PMID: 34443404 PMCID: PMC8398983 DOI: 10.3390/molecules26164816] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 01/10/2023] Open
Abstract
Novel dyes were prepared by simple "click CuAAC" attachment of a triarylborane-alkyne to the azide side chain of an amino acid yielding triarylborane dye 1 which was conjugated with pyrene (dye 2) forming a triarylborane-pyrene FRET pair. In contrast to previous cationic triarylboranes, the novel neutral dyes interact only with proteins, while their affinity to DNA/RNA is completely abolished. Both the reference triarylborane amino acid and triarylborane-pyrene conjugate bind to BSA and the hDPP III enzyme with high affinities, exhibiting a strong (up to 100-fold) fluorescence increase, whereby the triarylborane-pyrene conjugate additionally retained FRET upon binding to the protein. Furthermore, the triarylborane dyes, upon binding to the hDPP III enzyme, did not impair its enzymatic activity under a wide range of experimental conditions, thus being the first non-covalent fluorimetric markers for hDPP III, also applicable during enzymatic reactions with hDPP III substrates.
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Affiliation(s)
- Željka Ban
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; (Ž.B.); (Z.K.)
| | - Zrinka Karačić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; (Ž.B.); (Z.K.)
| | - Sanja Tomić
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; (Ž.B.); (Z.K.)
- Correspondence: (S.T.); (I.P.); Tel.: +385-1-4571-251 (S.T.); +385-1-4571-326 (I.P.)
| | - Hashem Amini
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany; (H.A.); (T.B.M.)
| | - Todd B. Marder
- Institut für Anorganische Chemie and Institute for Sustainable Chemistry & Catalysis with Boron, Julius-Maximilians-Universität Würzburg, 97074 Würzburg, Germany; (H.A.); (T.B.M.)
| | - Ivo Piantanida
- Division of Organic Chemistry & Biochemistry, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; (Ž.B.); (Z.K.)
- Correspondence: (S.T.); (I.P.); Tel.: +385-1-4571-251 (S.T.); +385-1-4571-326 (I.P.)
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5
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Komeno M, Pang X, Shimizu A, Molla MR, Yasuda-Yamahara M, Kume S, Rahman NIA, Soh JEC, Nguyen LKC, Ahmat Amin MKB, Kokami N, Sato A, Asano Y, Maegawa H, Ogita H. Cardio- and reno-protective effects of dipeptidyl peptidase III in diabetic mice. J Biol Chem 2021; 296:100761. [PMID: 33971198 PMCID: PMC8167299 DOI: 10.1016/j.jbc.2021.100761] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/27/2021] [Accepted: 05/05/2021] [Indexed: 01/09/2023] Open
Abstract
Diabetes mellitus (DM) causes injury to tissues and organs, including to the heart and kidney, resulting in increased morbidity and mortality. Thus, novel potential therapeutics are continuously required to minimize DM-related organ damage. We have previously shown that dipeptidyl peptidase III (DPPIII) has beneficial roles in a hypertensive mouse model, but it is unknown whether DPPIII has any effects on DM. In this study, we found that intravenous administration of recombinant DPPIII in diabetic db/db mice for 8 weeks suppressed the DM-induced cardiac diastolic dysfunctions and renal injury without alteration of the blood glucose level. This treatment inhibited inflammatory cell infiltration and fibrosis in the heart and blocked the increase in albuminuria by attenuating the disruption of the glomerular microvasculature and inhibiting the effacement of podocyte foot processes in the kidney. The beneficial role of DPPIII was, at least in part, mediated by the cleavage of a cytotoxic peptide, named Peptide 2, which was increased in db/db mice compared with normal mice. This peptide consisted of nine amino acids, was a digested fragment of complement component 3 (C3), and had an anaphylatoxin-like effect determined by the Miles assay and chemoattractant analysis. The effect was dependent on its interaction with the C3a receptor and protein kinase C-mediated RhoA activation downstream of the receptor in endothelial cells. In conclusion, DPPIII plays a protective role in the heart and kidney in a DM animal model through cleavage of a peptide that is a part of C3.
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Affiliation(s)
- Masahiro Komeno
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Xiaoling Pang
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan; Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China
| | - Akio Shimizu
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Md Rasel Molla
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | | | - Shinji Kume
- Department of Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Nor Idayu A Rahman
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Joanne Ern Chi Soh
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Le Kim Chi Nguyen
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Mohammad Khusni B Ahmat Amin
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Nao Kokami
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Akira Sato
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Hiroshi Maegawa
- Department of Medicine, Shiga University of Medical Science, Otsu, Japan
| | - Hisakazu Ogita
- Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Otsu, Japan.
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6
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Menale C, Robinson LJ, Palagano E, Rigoni R, Erreni M, Almarza AJ, Strina D, Mantero S, Lizier M, Forlino A, Besio R, Monari M, Vezzoni P, Cassani B, Blair HC, Villa A, Sobacchi C. Absence of Dipeptidyl Peptidase 3 Increases Oxidative Stress and Causes Bone Loss. J Bone Miner Res 2019; 34:2133-2148. [PMID: 31295380 PMCID: PMC7203631 DOI: 10.1002/jbmr.3829] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/26/2019] [Accepted: 07/06/2019] [Indexed: 12/29/2022]
Abstract
Controlling oxidative stress through the activation of antioxidant pathways is crucial in bone homeostasis, and impairments of the cellular defense systems involved contribute to the pathogenesis of common skeletal diseases. In this work we focused on the dipeptidyl peptidase 3 (DPP3), a poorly investigated ubiquitous zinc-dependent exopeptidase activating the Keap1-Nrf2 antioxidant pathway. We showed Dpp3 expression in bone and, to understand its role in this compartment, we generated a Dpp3 knockout (KO) mouse model and specifically investigated the skeletal phenotype. Adult Dpp3 KO mice showed a mild growth defect, a significant increase in bone marrow cellularity, and bone loss mainly caused by increased osteoclast activity. Overall, in the mouse model, lack of DPP3 resulted in sustained oxidative stress and in alterations of bone microenvironment favoring the osteoclast compared to the osteoblast lineage. Accordingly, in vitro studies revealed that Dpp3 KO osteoclasts had an inherent increased resorptive activity and ROS production, which on the other hand made them prone to apoptosis. Moreover, absence of DPP3 augmented bone loss after estrogen withdrawal in female mice, further supporting its relevance in the framework of bone pathophysiology. Overall, we show a nonredundant role for DPP3 in the maintenance of bone homeostasis and propose that DPP3 might represent a possible new osteoimmunological player and a marker of human bone loss pathology. © 2019 American Society for Bone and Mineral Research.
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Affiliation(s)
- Ciro Menale
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Lisa J Robinson
- Department of Pathology, West Virginia University, Morgantown, WV, USA
| | - Eleonora Palagano
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Rosita Rigoni
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Marco Erreni
- Unit of Advanced Optical Microscopy, Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Alejandro J Almarza
- Department of Oral Biology, Department of Bioengineering, McGowan Institute of Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Dario Strina
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Stefano Mantero
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Michela Lizier
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Antonella Forlino
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy
| | - Roberta Besio
- Department of Molecular Medicine, Unit of Biochemistry, University of Pavia, Pavia, Italy
| | - Marta Monari
- Clinical Investigation Laboratory, Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Paolo Vezzoni
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Barbara Cassani
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Harry C Blair
- Veterans' Affairs Medical Center and Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Anna Villa
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
| | - Cristina Sobacchi
- Consiglio Nazionale delle Ricerche-Istituto di Ricerca Genetica e Biomedica (CNR-IRGB), Milan Unit, Milan, Italy.,Humanitas Clinical and Research Center-Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Rozzano, Italy
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7
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Ćehić M, Suć Sajko J, Karačić Z, Piotrowski P, Šmidlehner T, Jerić I, Schmuck C, Piantanida I, Tomić S. The guanidiniocarbonylpyrrole-fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition. J Biomol Struct Dyn 2019; 38:3790-3800. [PMID: 31496375 DOI: 10.1080/07391102.2019.1664936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Study of seven new guanidiniocarbonylpyrrole (GCP)-fluorophore conjugates interactions with dipeptidyl peptidase III (DPP III) showed that all compounds bind strongly (Ks ≈ µM) to enzyme active site, but with very different fluorimetric response (varying from quenching to strong increase), dependent on the fluorophore type and intramolecular pre-organisation of molecule. Positively charged lysine side chain improved significantly compound solubility but diminished fluorescence increase upon DPP III binding and completely abolished inhibitory effect on DPP III activity, whereas linker-neutral analogues showed stronger emission increase and were efficient enzyme inhibitors. By far the best fluorimetric response and inhibitive properties showed cyanine-GCP analogue, thus being promising lead compound for both enzyme sensing and bio-activity inhibiting (theragnostic) studies of DPP III in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen, Germany
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8
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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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9
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Purification, kinetic and functional characterization of membrane bound dipeptidyl peptidase-III from NCDC 252: a probiotic lactic acid bacteria. Mol Biol Rep 2018; 45:973-986. [PMID: 30039431 DOI: 10.1007/s11033-018-4245-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/08/2018] [Indexed: 01/14/2023]
Abstract
Pediococcus acidilactici is a probiotic lactic acid bacteria possessing studied in-vitro probiotic properties. Study of membrane proteins is crucial in developing technological and health applications of probiotic bacteria. Genome analysis of Pediococcus acidilactici revealed about more than 60 proteases/peptidases which need characterization. Dipeptidyl peptidase-III (DPP-III) is studied for first time in prokaryotes and it is a membrane protein in P. acidilactici that has been purified to apparent homogeneity. The enzyme was purified 81.66 fold with 36.75% yield. The specific activity of purified DPP-III was 202.67 U/mg. The protein moved as single band on native PAGE. The purity was also confirmed by in-situ gel assay. However SDS-PAGE analysis revealed it as high molecular weight heterotetramer with molecular weight of 108 kDa. The enzyme was maximally active at pH 8.5 and at 37 C. Purified DPP-III specifically hydrolyzed Arg-Arg-4-βNA with micromolar affinity (Km = 9.0 µM) and none of studied endopeptidase and monopeptidase substrate was hydrolyzed. Inhibition study revealed purified DPP-III to be a serine protease with involvement of metal ion at active site. The significance of this enzyme as membrane protein is yet to be studied.
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10
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Sabljić I, Tomin M, Matovina M, Sučec I, Tomašić Paić A, Tomić A, Abramić M, Tomić S. The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. PLoS One 2018; 13:e0192488. [PMID: 29420664 PMCID: PMC5805324 DOI: 10.1371/journal.pone.0192488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/24/2018] [Indexed: 12/14/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.
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Affiliation(s)
- Igor Sabljić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marko Tomin
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Iva Sučec
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, 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
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail:
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11
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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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12
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Cruz-Diaz N, Wilson BA, Pirro NT, Brosnihan KB, Marshall AC, Chappell MC. Identification of dipeptidyl peptidase 3 as the Angiotensin-(1-7) degrading peptidase in human HK-2 renal epithelial cells. Peptides 2016; 83:29-37. [PMID: 27315786 PMCID: PMC5500233 DOI: 10.1016/j.peptides.2016.06.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 01/08/2023]
Abstract
Angiotensin-(1-7) (Ang-(1-7)) is expressed within the kidney and exhibits renoprotective actions that antagonize the inflammatory, fibrotic and pro-oxidant effects of the Ang II-AT1 receptor axis. We previously identified a peptidase activity from sheep brain, proximal tubules and human HK-2 proximal tubule cells that metabolized Ang-(1-7); thus, the present study isolated and identified the Ang-(1-7) peptidase. Utilizing ion exchange and hydrophobic interaction chromatography, a single 80kDa protein band on SDS-PAGE was purified from HK-2 cells. The 80kDa band was excised, the tryptic digest peptides analyzed by LC-MS and a protein was identified as the enzyme dipeptidyl peptidase 3 (DPP 3, EC: 3.4.14.4). A human DPP 3 antibody identified a single 80kDa band in the purified enzyme preparation identical to recombinant human DPP 3. Both the purified Ang-(1-7) peptidase and DPP 3 exhibited an identical hydrolysis profile of Ang-(1-7) and both activities were abolished by the metallopeptidase inhibitor JMV-390. DPP 3 sequentially hydrolyzed Ang-(1-7) to Ang-(3-7) and rapidly converted Ang-(3-7) to Ang-(5-7). Kinetic analysis revealed that Ang-(3-7) was hydrolyzed at a greater rate than Ang-(1-7) [17.9 vs. 5.5 nmol/min/μg protein], and the Km for Ang-(3-7) was lower than Ang-(1-7) [3 vs. 12μM]. Finally, chronic treatment of the HK-2 cells with 20nM JMV-390 reduced intracellular DPP 3 activity and tended to augment the cellular levels of Ang-(1-7). We conclude that DPP 3 may influence the cellular expression of Ang-(1-7) and potentially reflect a therapeutic target to augment the actions of the peptide.
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Affiliation(s)
- Nildris Cruz-Diaz
- Department of Surgery, Hypertension & Vascular Research, Cardiovascular Sciences Center, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Bryan A Wilson
- Department of Surgery, Hypertension & Vascular Research, Cardiovascular Sciences Center, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - Nancy T Pirro
- Department of Surgery, Hypertension & Vascular Research, Cardiovascular Sciences Center, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | - K Bridget Brosnihan
- Department of Surgery, Hypertension & Vascular Research, Cardiovascular Sciences Center, Wake Forest University School of Medicine, Winston-Salem, NC, United States
| | | | - Mark C Chappell
- Department of Surgery, Hypertension & Vascular Research, Cardiovascular Sciences Center, Wake Forest University School of Medicine, Winston-Salem, NC, United States.
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13
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Kumar P, Reithofer V, Reisinger M, Wallner S, Pavkov-Keller T, Macheroux P, Gruber K. Substrate complexes of human dipeptidyl peptidase III reveal the mechanism of enzyme inhibition. Sci Rep 2016; 6:23787. [PMID: 27025154 PMCID: PMC4824452 DOI: 10.1038/srep23787] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Accepted: 03/15/2016] [Indexed: 02/02/2023] Open
Abstract
Human dipeptidyl-peptidase III (hDPP III) is a zinc-dependent hydrolase cleaving dipeptides off the N-termini of various bioactive peptides. Thus, the enzyme is likely involved in a number of physiological processes such as nociception and is also implicated in several forms of cancer. We present high-resolution crystal structures of hDPP III in complex with opioid peptides (Met-and Leu-enkephalin, endomorphin-2) as well as with angiotensin-II and the peptide inhibitor IVYPW. These structures confirm the previously reported large conformational change of the enzyme upon ligand binding and show that the structure of the closed conformation is independent of the nature of the bound peptide. The overall peptide-binding mode is also conserved ensuring the correct positioning of the scissile peptide bond with respect to the catalytic zinc ion. The structure of the angiotensin-II complex shows, how longer peptides are accommodated in the binding cleft of hDPP III. Differences in the binding modes allow a distinction between real substrates and inhibitory peptides or “slow” substrates. The latter displace a zinc bound water molecule necessitating the energetically much less favoured anhydride mechanism as opposed to the favoured promoted-water mechanism. The structural data also form the necessary framework for the design of specific hDPP III inhibitors.
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Affiliation(s)
- Prashant Kumar
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria
| | - Viktoria Reithofer
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria
| | - Manuel Reisinger
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria
| | - Silvia Wallner
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria
| | - Tea Pavkov-Keller
- ACIB - Austrian Centre of Industrial Biotechnology, Petersgasse 14, 8010 Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/2, 8010 Graz, Austria.,BioTechMed-Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Humboldtstraße 50/3, 8010 Graz, Austria.,BioTechMed-Graz, Austria
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14
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Sobočanec S, Filić V, Matovina M, Majhen D, Šafranko ŽM, Hadžija MP, Krsnik Ž, Kurilj AG, Šarić A, Abramić M, Balog T. Prominent role of exopeptidase DPP III in estrogen-mediated protection against hyperoxia in vivo. Redox Biol 2016; 8:149-59. [PMID: 26774752 PMCID: PMC4732022 DOI: 10.1016/j.redox.2016.01.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 01/05/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023] Open
Abstract
A number of age-related diseases have a low incidence in females, which is attributed to a protective effect of sex hormones. For instance, the female sex hormone estrogen (E2) has a well established cytoprotective effect against oxidative stress, which strongly contributes to ageing. However, the mechanism by which E2 exerts its protective activity remains elusive. In this study we address the question whether the E2-induced protective effect against hyperoxia is mediated by the Nrf-2/Keap-1 signaling pathway. In particular, we investigate the E2-induced expression and cellular distribution of DPP III monozinc exopeptidase, a member of the Nrf-2/Keap-1 pathway, upon hyperoxia treatment. We find that DPP III accumulates in the nucleus in response to hyperoxia. Further, we show that combined induction of hyperoxia and E2 administration have an additive effect on the nuclear accumulation of DPP III. The level of nuclear accumulation of DPP III is comparable to nuclear accumulation of Nrf-2 in healthy female mice exposed to hyperoxia. In ovariectomized females exposed to hyperoxia, supplementation of E2 induced upregulation of DPP III, Ho-1, Sirt-1 and downregulation of Ppar-γ. While other cytoprotective mechanisms cannot be excluded, these findings demonstrate a prominent role of DPP III, along with Sirt-1, in the E2-mediated protection against hyperoxia. DPP III accumulates in the nucleus in response to hyperoxia. Additive effect of hyperoxia and E2 on nuclear accumulation of DPP III is observed. Protective effect of E2 is associated with increased DPP III, Ho-1 and Sirt-1.
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Affiliation(s)
- Sandra Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Vedrana Filić
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | | | - Željka Krsnik
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - Andrea Gudan Kurilj
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Šarić
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Tihomir Balog
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
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15
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Abramić M, Karačić Z, Šemanjski M, Vukelić B, Jajčanin-Jozić N. Aspartate 496 from the subsite S2 drives specificity of human dipeptidyl peptidase III. Biol Chem 2015; 396:359-66. [PMID: 25581752 DOI: 10.1515/hsz-2014-0247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 01/02/2015] [Indexed: 11/15/2022]
Abstract
Human dipeptidyl peptidase III (hDPP III) is a member of the M49 metallopeptidase family, which is involved in intracellular protein catabolism and oxidative stress response. To investigate the structural basis of hDPP III preference for diarginyl arylamide, using site-directed mutagenesis, we altered its S2 subsite to mimic the counterpart in yeast enzyme. Kinetic studies revealed that the single mutant D496G lost selectivity due to the increase of the Km value. The D496G, but not S504G, showed significantly decreased binding of peptides with N-terminal arginine, and of tynorphin. The results obtained identify Asp496 as an important determinant of human DPP III substrate specificity.
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16
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Mačak Šafranko Ž, Sobočanec S, Šarić A, Jajčanin-Jozić N, Krsnik Ž, Aralica G, Balog T, Abramić M. The effect of 17β-estradiol on the expression of dipeptidyl peptidase III and heme oxygenase 1 in liver of CBA/H mice. J Endocrinol Invest 2015; 38:471-9. [PMID: 25432329 DOI: 10.1007/s40618-014-0217-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Accepted: 11/19/2014] [Indexed: 12/26/2022]
Abstract
BACKGROUND 17β-estradiol (E₂) has well-established cardioprotective, antioxidant and neuroprotective role, and exerts a vast range of biological effects in both sexes. Dipeptidyl peptidase III (DPP III) is protease involved as activator in Keap1-Nrf2 signalling pathway, which is important in cellular defense to oxidative and electrophilic stress. It is generally accepted that oxidative stress is crucial in promoting liver diseases. OBJECTIVE To examine the effect of E₂ on the expression of DPP III and haeme oxygenase 1 (HO-1) in liver of adult CBA/H mice of both sexes. METHODS Gene and protein expressions of studied enzymes were determined by quantitative real-time PCR and Western blot analysis. Immunohistochemistry was performed to analyse the localization of both proteins in different liver cell types. RESULTS Ovariectomy diminished expression of DPP III and HO-1 proteins. E₂ administration abolished this effect, and even increased these proteins above the control. A significant enhancement in DPP III protein was found in E₂-treated males, as well. A decrease in the expression of HO-1, but not of the DPP III gene, was detected in the liver of ovariectomized females. HO-1 protein was found localized in the pericentral areas of hepatic lobules (Kupffer cells and hepatocytes), whilst DPP III showed a uniform distribution within hepatic tissue. CONCLUSIONS We demonstrate for the first time that E₂ influences the protein level of DPP III in vivo, and confirm earlier finding on HO-1 gene upregulation by 17β-estradiol. These results additionally confer new insights into complexity of protective action of E₂.
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Affiliation(s)
- Ž Mačak Šafranko
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - S Sobočanec
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia.
| | - A Šarić
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - N Jajčanin-Jozić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ž Krsnik
- Croatian Institute for Brain Research, University of Zagreb School of Medicine, Zagreb, Croatia
| | - G Aralica
- Department of Pathology, Medical School University of Zagreb and University Hospital, Dubrava, Zagreb, Croatia
| | - T Balog
- Division of Molecular Medicine, Ruđer Bošković Institute, Zagreb, Croatia
| | - M Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
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17
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Jajčanin-Jozić N, Abramić M. Hydrolysis of dipeptide derivatives reveals the diversity in the M49 family. Biol Chem 2014; 394:767-71. [PMID: 23362197 DOI: 10.1515/hsz-2012-0347] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 01/14/2013] [Indexed: 11/15/2022]
Abstract
Dipeptidyl peptidase III, a metallopeptidase of the M49 family, was first identified (in the pituitary) by its specific cleavage of diarginyl arylamides, which have been used as preferred assay substrates until now. Here we examined the activity of the yeast and human dipeptidyl peptidase III in parallel. The human enzyme preferred Arg(2)-β-naphthylamide and showed 620-fold higher k(cat)/K(m) for this substrate. In contrast, the yeast enzyme did not display a preference for any of the X-Arg-β-naphthylamide analyzed. The replacement of Gly(505) with Asp, resulted in a less active, but more selective, yeast enzyme form. These results indicate diversity in cleavage specificity in the M49 family.
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Affiliation(s)
- Nina Jajčanin-Jozić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10002 Zagreb, Croatia
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18
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Jajčanin-Jozić N, Tomić S, Abramić M. Importance of the three basic residues in the vicinity of the zinc-binding motifs for the activity of the yeast dipeptidyl peptidase III. ACTA ACUST UNITED AC 2013; 155:43-50. [DOI: 10.1093/jb/mvt093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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19
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Jodha D, Attri P, Khaket TP, Singh J. Isolation, purification and biochemical characterization of dipeptidyl peptidase-III from germinated Vigna radiata seeds. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.02.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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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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21
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Cyclic enediyne–amino acid chimeras as new aminopeptidase N inhibitors. Amino Acids 2012; 43:2087-100. [DOI: 10.1007/s00726-012-1292-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/03/2012] [Indexed: 10/28/2022]
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22
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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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23
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Prajapati SC, Chauhan SS. Dipeptidyl peptidase III: a multifaceted oligopeptide N-end cutter. FEBS J 2011; 278:3256-76. [DOI: 10.1111/j.1742-4658.2011.08275.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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24
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Jajcanin-Jozić N, Deller S, Pavkov T, Macheroux P, Abramić M. Identification of the reactive cysteine residues in yeast dipeptidyl peptidase III. Biochimie 2009; 92:89-96. [PMID: 19825391 DOI: 10.1016/j.biochi.2009.09.014] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2009] [Accepted: 09/24/2009] [Indexed: 11/24/2022]
Abstract
Dipeptidyl peptidases III (DPPs III) form a distinct metallopeptidase family characterized by the unique HEXXGH motif. High susceptibility to inactivation by organomercurials suggests the presence of a reactive cysteine residue(s) in, or close to, their active site. Yeast DPP III contains five Cys, none of which is absolutely conserved within the family. In order to identify reactive residue(s), site-directed mutagenesis on yeast His(6)-tagged DPP III was employed to substitute specifically all five cysteine residues to serine. The variant enzymes thus obtained were enzymatically active and showed an overall structure not greatly affected by the mutations as judged by circular dichroism. Analysis by native and SDS-PAGE under non-reducing conditions revealed the existence of a monomeric and dimeric form in all DPP III proteins except in the C130S, implying that dimerization of yeast DPP III is mediated by the surface-exposed cysteine 130. The investigation of the effect of thiol reagent 4,4'-dithiodipyridine (DTDP) on all five Cys to Ser single protein variants showed that Cys639 and Cys518 are more reactive than the remainder. Only the C639S mutant protein displayed the remarkable resistance against p-hydroxy-mercuribenzoate (pHMB) indicating that modification of Cys639 is responsible for the fast inactivation of yeast DPP III by this sulfhydryl reagent.
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25
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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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26
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Dhanda S, Singh H, Singh J, Singh TP. Functional characterization and specific effects of various peptides on enzymatic activity of a DPP-III homologue from goat brain. J Enzyme Inhib Med Chem 2008; 23:174-81. [DOI: 10.1080/14756360701450996] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Suman Dhanda
- Department of Biochemistry, Kurukshetra University, Kurukshetra, -136119, India
| | - Hari Singh
- Department of Biochemistry, Kurukshetra University, Kurukshetra, -136119, India
| | - Jasbir Singh
- Department of Biochemistry, Kurukshetra University, Kurukshetra, -136119, India
| | - Tej P. Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India
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27
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Cicin-Sain L, Simaga S, Froebe A, Abramić M. Central aminopeptidase and serotonin system activities: possible relationship. Neuropeptides 2008; 42:435-40. [PMID: 18547641 DOI: 10.1016/j.npep.2008.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2008] [Revised: 04/24/2008] [Accepted: 04/25/2008] [Indexed: 11/22/2022]
Abstract
The co-localization of serotonin (5-hydroxytryptamine, 5HT) and neuroactive peptides in the same neuron points to the importance of interactions between serotonergic and peptidergic systems in maintaining body homeostasis. In this work, we used an original genetic rat model to search for possible interrelations between 5HT system functioning and the activities of aminopeptidases, i.e. enzymes which are the key regulators of (neuro)peptides level/function. The activities of three cytosolic exopeptidases: alanyl aminopeptidase (alanyl-AP), arginyl aminopeptidase (arginyl-AP) and dipeptidyl peptidase III (DPP III) were measured in brains and peripheral tissues of the sublines of rats with constitutionally upregulated/downregulated 5HT transporter activity. These rat sublines, termed as high-5HT and low-5HT subline, have been obtained previously by selective breeding for the extreme values of platelet 5HT level and velocity of 5HT uptake. Besides in the periphery they show marked alterations also in brain 5HT function, indicating the differences in central 5HT transmission/homeostasis. In this study, we have found that animals from the high-5HT subline have significantly lower activity of brain alanyl-AP (p<0.05) and arginyl-AP (p<0.01) as compared to control animals. No other differences were noticed regardless of the 5HT subline, investigated organ or analyzed aminopeptidase. Results suggest that the constitutional upregulation of serotonergic activity may be related to a lowered brain cytosolic aminopeptidase activity which may have an influence on the cleavage of their physiological substrates.
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Affiliation(s)
- L Cicin-Sain
- Department of Molecular Biology, "Rudjer Bosković" Institute, Bijenicka 54, HR-10000 Zagreb, Croatia.
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28
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Baral PK, Jajcanin-Jozić N, Deller S, Macheroux P, Abramić M, Gruber K. The first structure of dipeptidyl-peptidase III provides insight into the catalytic mechanism and mode of substrate binding. J Biol Chem 2008; 283:22316-24. [PMID: 18550518 DOI: 10.1074/jbc.m803522200] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Dipeptidyl-peptidases III (DPP III) are zinc-dependent enzymes that specifically cleave the first two amino acids from the N terminus of different length peptides. In mammals, DPP III is associated with important physiological functions and is a potential biomarker for certain types of cancer. Here, we present the 1.95-A crystal structure of yeast DPP III representing the prototype for the M49 family of metallopeptidases. It shows a novel fold with two domains forming a wide cleft containing the catalytic metal ion. DPP III exhibits no overall similarity to other metallopeptidases, such as thermolysin and neprilysin, but zinc coordination and catalytically important residues are structurally conserved. Substrate recognition is accomplished by a binding site for the N terminus of the peptide at an appropriate distance from the metal center and by a series of conserved arginine residues anchoring the C termini of different length substrates.
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Affiliation(s)
- Pravas Kumar Baral
- Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria
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29
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Salopek-Sondi B, Vukelić B, Spoljarić J, Simaga S, Vujaklija D, Makarević J, Jajcanin N, Abramić M. Functional tyrosine residue in the active center of human dipeptidyl peptidase III. Biol Chem 2008; 389:163-7. [PMID: 18163885 DOI: 10.1515/bc.2008.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract Human dipeptidyl peptidase III (DPP III) is a member of the metallopeptidase family M49 with an implied role in the pain-modulatory system and endogenous defense against oxidative stress. Here, we report the heterologous expression of human DPP III and the site-directed mutagenesis results which demonstrate a functional role for Tyr318 at the active site of this enzyme. The substitution of Tyr318 to Phe decreased kcat by two orders of magnitude without altering the binding affinity of substrate, or of a competitive hydroxamate inhibitor designed to interact with S1 and S2 subsites. The results indicate that the conserved tyrosine could be involved in transition state stabilization during the catalytic action of M49 peptidases.
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Affiliation(s)
- Branka Salopek-Sondi
- Division of Molecular Biology, Ruder Bosković Institute, Bijenicka cesta 54, HR-10002 Zagreb, Croatia
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Barsun M, Jajcanin N, Vukelić B, Spoljarić J, Abramić M. Human dipeptidyl peptidase III acts as a post-proline-cleaving enzyme on endomorphins. Biol Chem 2007; 388:343-8. [PMID: 17338643 DOI: 10.1515/bc.2007.039] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Dipeptidyl peptidase III (DPP III) is a zinc exopeptidase with an implied role in the mammalian pain-modulatory system owing to its high affinity for enkephalins and localisation in the superficial laminae of the spinal cord dorsal horn. Our study revealed that this human enzyme hydrolyses opioid peptides belonging to three new groups, endomorphins, hemorphins and exorphins. The enzymatic hydrolysis products of endomorphin-1 were separated and quantified by capillary electrophoresis and the kinetic parameters were determined for human DPP III and rat DPP IV. Both peptidases cleave endomorphin-1 at comparable rates, with liberation of the N-terminal Tyr-Pro. This is the first evidence of DPP III acting as an endomorphin-cleaving enzyme.
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Affiliation(s)
- Marina Barsun
- PLIVA Research and Development Ltd., Prilaz baruna Filipovića 25, 10000 Zagreb, Croatia
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31
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Agić D, Hranjec M, Jajcanin N, Starcević K, Karminski-Zamola G, Abramić M. Novel amidino-substituted benzimidazoles: Synthesis of compounds and inhibition of dipeptidyl peptidase III. Bioorg Chem 2007; 35:153-69. [PMID: 17174378 DOI: 10.1016/j.bioorg.2006.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Revised: 10/22/2006] [Accepted: 11/03/2006] [Indexed: 11/19/2022]
Abstract
Dipeptidyl peptidase III (DPP III), also known as enkephalinase B, is a zinc-hydrolase with an indicated role in the mammalian pain modulatory system. In order to find a potent antagonist of this enzyme, we synthesized and screened the effect of a small set of benzimidazole derivatives on its activity. To improve the inhibitory potential, a cyclobutane ring was introduced as rigid conformation support to the diamidino substituted dibenzimidazoles. Two such compounds (1' and 4') from the group of cyclobutane derivatives containing amidino-substituted benzimidazole moieties, obtained by photochemical cyclization in water and by respecting rules of the "green chemistry" approach, were found to be strong DPP III inhibitors, with IC(50) value below 5 microM. Compound 1' displayed time-dependent inhibition towards human DPP III, characterized by the second-order rate constant of 6924+/-549 M(-1)min(-1) (K(i)=0.20 microM). The peptide substrate valorphin protected the enzyme from inactivation by 1'.
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Affiliation(s)
- Dejan Agić
- Department of Chemistry, Faculty of Agriculture, The Josip Juraj Strossmayer University, Trg Sv. Trojstva 3, P.O. Box 719, HR-31107 Osijek, Croatia
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32
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Dhanda S, Singh H, Singh J, Singh TP. Isolation, purification and characterization of a DPP-III homologue from goat brain. Protein Expr Purif 2007; 52:297-305. [PMID: 17182254 DOI: 10.1016/j.pep.2006.10.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2006] [Revised: 10/09/2006] [Accepted: 10/10/2006] [Indexed: 11/16/2022]
Abstract
A dipeptidyl peptidase (DPP) from goat brain has been purified. The purified enzyme showed a single band on sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE). It is a monomer with molecular weight of 69kDa with a pI of 4.5. The K(m) was estimated to be 39microM for Arg-Arg-4-methoxy-beta-naphthylamide (Arg-Arg-4mbetaNA). This enzyme is strongly inhibited by commonly used metallochelators and sulfhydryl reagents. Among various beta-naphthylamides examined, Arg-Arg-4mbetaNA was the most rapidly hydrolyzed substrate. Although, initially it was thought to be the DPP-III but on the basis of its molecular weight and inhibition studies, it was concluded that this enzyme is a functional homologue of DPP-III.
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Affiliation(s)
- Suman Dhanda
- Department of Biochemistry, Kurukshetra University, Kurukshetra 136119, Haryana, India.
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