1
|
Jiang L, Liu S, Jia X, Gong Q, Wen X, Lu W, Yang J, Wu X, Wang X, Suo Y, Li Y, Uesugi M, Qu ZB, Tan M, Lu X, Zhou L. ABPP-CoDEL: Activity-Based Proteome Profiling-Guided Discovery of Tyrosine-Targeting Covalent Inhibitors from DNA-Encoded Libraries. J Am Chem Soc 2023; 145:25283-25292. [PMID: 37857329 DOI: 10.1021/jacs.3c08852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
DNA-encoded chemical library (DEL) has been extensively used for lead compound discovery for decades in academia and industry. Incorporating an electrophile warhead into DNA-encoded compounds recently permitted the discovery of covalent ligands that selectively react with a particular cysteine residue. However, noncysteine residues remain underexplored as modification sites of covalent DELs. Herein, we report the design and utility of tyrosine-targeting DELs of 67 million compounds. Proteome-wide reactivity analysis of tyrosine-reactive sulfonyl fluoride (SF) covalent probes suggested three enzymes (phosphoglycerate mutase 1, glutathione s-transferase 1, and dipeptidyl peptidase 3) as models of tyrosine-targetable proteins. Enrichment with SF-functionalized DELs led to the identification of a series of tyrosine-targeting covalent inhibitors of the model enzymes. In-depth mechanistic investigation revealed their novel modes of action and reactive ligand-accessible hotspots of the enzymes. Our strategy of combining activity-based proteome profiling and covalent DEL enrichment (ABPP-CoDEL), which generated selective covalent binders against a variety of target proteins, illustrates the potential use of this methodology in further covalent drug discovery.
Collapse
Affiliation(s)
- Lulu Jiang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Sixiu Liu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xinglong Jia
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Qinting Gong
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xin Wen
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weiwei Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jintong Yang
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xinyuan Wu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Xuan Wang
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Yanrui Suo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yilin Li
- National Facility for Protein Science in Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Motonari Uesugi
- School of Pharmacy, Fudan University, Shanghai 201203, China
- Institute for Chemical Research and Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Zhi-Bei Qu
- School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Minjia Tan
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan, Guangdong 528400, China
| | - Xiaojie Lu
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Lu Zhou
- School of Pharmacy, Fudan University, Shanghai 201203, China
| |
Collapse
|
2
|
Liao CC, Wang YS, Pi WC, Wang CH, Wu YM, Chen WY, Hsia KC. Structural convergence endows nuclear transport receptor Kap114p with a transcriptional repressor function toward TATA-binding protein. Nat Commun 2023; 14:5518. [PMID: 37684250 PMCID: PMC10491584 DOI: 10.1038/s41467-023-41206-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 08/24/2023] [Indexed: 09/10/2023] Open
Abstract
The transcription factor TATA-box binding protein (TBP) modulates gene expression in nuclei. This process requires the involvement of nuclear transport receptors, collectively termed karyopherin-β (Kap-β) in yeast, and various regulatory factors. In previous studies we showed that Kap114p, a Kap-β that mediates nuclear import of yeast TBP (yTBP), modulates yTBP-dependent transcription. However, how Kap114p associates with yTBP to exert its multifaceted functions has remained elusive. Here, we employ single-particle cryo-electron microscopy to determine the structure of Kap114p in complex with the core domain of yTBP (yTBPC). Remarkably, Kap114p wraps around the yTBPC N-terminal lobe, revealing a structure resembling transcriptional regulators in complex with TBP, suggesting convergent evolution of the two protein groups for a common function. We further demonstrate that Kap114p sequesters yTBP away from promoters, preventing a collapse of yTBP dynamics required for yeast responses to environmental stress. Hence, we demonstrate that nuclear transport receptors represent critical elements of the transcriptional regulatory network.
Collapse
Affiliation(s)
- Chung-Chi Liao
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, 11490, Taiwan
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Sen Wang
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wen-Chieh Pi
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan
| | - Chun-Hsiung Wang
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Yi-Min Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan
| | - Wei-Yi Chen
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
- Cancer and Immunology Research Center, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Kuo-Chiang Hsia
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and National Defense Medical Center, Taipei, 11490, Taiwan.
- Institute of Molecular Biology, Academia Sinica, Taipei, 11529, Taiwan.
- Institute of Biochemistry and Molecular Biology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| |
Collapse
|
3
|
Agić D, Karnaš M, Tomić S, Komar M, Karačić Z, Rastija V, Bešlo D, Šubarić D, Molnar M. Experimental and computational evaluation of dipeptidyl peptidase III inhibitors based on quinazolinone-Schiff's bases. J Biomol Struct Dyn 2023; 41:7567-7581. [PMID: 36106968 DOI: 10.1080/07391102.2022.2123044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that sequentially hydrolyzes biologically active peptides by cleaving dipeptides from their N-termini. Although its fundamental role is not been fully elucidated, human DPP III (hDPP III) has been recognized in several pathophysiological processes of interest for drug development. In this article 27 quinazolinone-Schiff's bases were studied for their inhibitory activity against hDPP III combining an in vitro experiment with a computational approach. The biochemical assay showed that most compounds exhibited inhibitory activity at the 100 μM concentration. The best QSAR model included descriptors from the following 2D descriptor groups: information content indices, 2D autocorrelations, and edge adjacency indices. Five compounds were found to be the most potent inhibitors with IC50 values below 10 µM, while molecular docking predicted that these compounds bind to the central enzyme cleft and interact with residues of the substrate binding subsites. Molecular dynamics simulations of the most potent inhibitor (IC50=0.96 µM) provided valuable information explaining the role of PHE109, ARG319, GLU327, GLU329, and ILE386 in the mechanism of the inhibitor binding and stabilization. This is the first study that gives insight into quinazolinone-Schiff's bases binding to this metalloenzyme.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Maja Karnaš
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Sanja Tomić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mario Komar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Zrinka Karačić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Vesna Rastija
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Drago Bešlo
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Domagoj Šubarić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Maja Molnar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| |
Collapse
|
4
|
Matić A, Šupljika F, Brkić H, Jurasović J, Karačić Z, Tomić S. Identification of an Additional Metal-Binding Site in Human Dipeptidyl Peptidase III. Int J Mol Sci 2023; 24:12747. [PMID: 37628928 PMCID: PMC10454320 DOI: 10.3390/ijms241612747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 08/27/2023] Open
Abstract
Dipeptidyl peptidase III (DPP III, EC 3.4.14.4) is a monozinc metalloexopeptidase that hydrolyzes dipeptides from the N-terminus of peptides consisting of three or more amino acids. Recently, DPP III has attracted great interest from scientists, and numerous studies have been conducted showing that it is involved in the regulation of various physiological processes. Since it is the only metalloenzyme among the dipeptidyl peptidases, we considered it important to study the process of binding and exchange of physiologically relevant metal dications in DPP III. Using fluorimetry, we measured the Kd values for the binding of Zn2+, Cu2+, and Co2+ to the catalytic site, and using isothermal titration calorimetry (ITC), we measured the Kd values for the binding of these metals to an additional binding site. The structure of the catalytic metal's binding site is known from previous studies, and in this work, the affinities for this site were calculated for Zn2+, Cu2+, Co2+, and Mn2+ using the QM approach. The structures of the additional binding sites for the Zn2+ and Cu2+ were also identified, and MD simulations showed that two Cu2+ ions bound to the catalytic and inhibitory sites exchanged less frequently than the Zn2+ ions bound to these sites.
Collapse
Affiliation(s)
- Antonia Matić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Filip Šupljika
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, Pierottijeva 6, 10000 Zagreb, Croatia;
| | - Hrvoje Brkić
- Faculty of Medicine, J. J. Strossmayer University of Osijek, 31000 Osijek, Croatia;
- Faculty of Dental Medicine and Health, J. J. Strossmayer University of Osijek, 31000 Osijek, Croatia
| | - Jasna Jurasović
- Analytical Toxicology and Mineral Metabolism Unit, Institute for Medical Research and Occupational Health, 10000 Zagreb, Croatia;
| | - Zrinka Karačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| |
Collapse
|
5
|
Innelli P, Lopizzo T, Paternò G, Bruno N, Radice RP, Bertini P, Marabotti A, Luzi G, Stabile E, Di Fazio A, Pittella G, Paternoster G. Dipeptidyl Amino-Peptidase 3 (DPP3) as an Early Marker of Severity in a Patient Population with Cardiogenic Shock. Diagnostics (Basel) 2023; 13:1350. [PMID: 37046568 PMCID: PMC10093224 DOI: 10.3390/diagnostics13071350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/29/2023] [Accepted: 04/02/2023] [Indexed: 04/14/2023] Open
Abstract
Dipeptidyl amino-peptidase 3 (DPP3) is an aminopeptidase that is released into circulation upon cell death. DPP3 is involved in the degradation of angiotensins, enkephalines, and endomorphines. It has been shown that circulating DPP3 (cDPP3) plasma concentration increases in cardiogenic shock (CS) patients and correlates with high mortality risk. Cardiogenic shock is a life-threatening syndrome associated with organ hypoperfusion. One of the common causes of CS is acute myocardial infarction (AMI). This study aimed to investigate if cDPP3 levels are associated with CS severity and the need for ventilation in patients suffering from CS. Fifteen patients with CS were included in this study. Six patients were invasively ventilated. The values of cDPP3 were higher in ventilated patients than in non-ventilated patients at admission, 3 h, and 24 h after admission in the intensive care unit. Patients with pulmonary hypertension at admission also showed high cDPP3 values at all time points. Furthermore, high cDPP3 levels were associated with reduced stroke volume. Our results suggest that cDPP3 could predict CS progression and guide therapy escalation.
Collapse
Affiliation(s)
- Pasquale Innelli
- Acute Cardiac Care Unit, San Carlo Hospital, 85100 Potenza, Italy
| | - Teresa Lopizzo
- Clinical Pathology and Microbiology, San Carlo Hospital, 85100 Potenza, Italy
| | - Giovanni Paternò
- Acute Cardiac Care Unit, San Carlo Hospital, 85100 Potenza, Italy
| | - Noemi Bruno
- Cardiac Intesive Care, San Camillo Forlanini, 00152 Rome, Italy
| | | | - Pietro Bertini
- Department of Anesthesia and Critical Care Medicine, Azienda Ospedaliero Universitaria Pisana, 56126 Pisa, Italy
| | - Alberto Marabotti
- Intensive Care Unit and Regional, ECMO Referral Centre, Azienda Ospedaliero-Universitaria Careggi, 50134 Florence, Italy
| | - Giampaolo Luzi
- Cardiac Surgery, San Carlo Hospital, 85100 Potenza, Italy
| | - Eugenio Stabile
- Acute Cardiac Care Unit, San Carlo Hospital, 85100 Potenza, Italy
| | - Aldo Di Fazio
- Regional Complex Intercompany Institute of Legal Medicine, San Carlo Hospital, 85100 Potenza, Italy
| | - Giuseppe Pittella
- Cardiac Resuscitation, Cardiovascular Anesthesia and Intensive Care, San Carlo Hospital, 85100 Potenza, Italy
| | - Gianluca Paternoster
- Cardiac Resuscitation, Cardiovascular Anesthesia and Intensive Care, San Carlo Hospital, 85100 Potenza, Italy
| |
Collapse
|
6
|
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.
Collapse
|
7
|
Structural and Functional Characterization of a New Bacterial Dipeptidyl Peptidase III Involved in Fruiting Body Formation in Myxobacteria. Int J Mol Sci 2022; 24:ijms24010631. [PMID: 36614072 PMCID: PMC9820243 DOI: 10.3390/ijms24010631] [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: 10/30/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) is a zinc-dependent enzyme that specifically hydrolyzes dipeptides from the N-terminal of different-length peptides, and it is involved in a number of physiological processes. Here, DPP III with an atypical pentapeptide zinc binding motif (HELMH) was identified from Corallococcus sp. EGB. It was shown that the activity of recombined CoDPP III was optimal at 50 °C and pH 7.0 with high thermostability up to 60 °C. Unique to CoDPP III, the crystal structure of the ligand-free enzyme was determined as a dimeric and closed form. The relatively small inter-domain cleft creates a narrower entrance to the substrate binding site and the unfavorable binding of the bulky naphthalene ring. The ectopic expression of CoDPP III in M. xanthus DK1622 resulted in a 12 h head start in fruiting body development compared with the wild type. Additionally, the A-signal prepared from the starving DK1622-CoDPP III rescued the developmental defect of the asgA mutant, and the fruiting bodies were more numerous and closely packed. Our data suggested that CoDPP III played a role in the fruiting body development of myxobacteria through the accumulation of peptides and amino acids to act as the A-signal.
Collapse
|
8
|
Ye P, Duan W, Leng YQ, Wang YK, Tan X, Wang WZ. DPP3: From biomarker to therapeutic target of cardiovascular diseases. Front Cardiovasc Med 2022; 9:974035. [PMID: 36312232 PMCID: PMC9605584 DOI: 10.3389/fcvm.2022.974035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiovascular disease is the leading cause of death globally among non-communicable diseases, which imposes a serious socioeconomic burden on patients and the healthcare system. Therefore, finding new strategies for preventing and treating cardiovascular diseases is of great significance in reducing the number of deaths and disabilities worldwide. Dipeptidyl peptidase 3 (DPP3) is the first zinc-dependent peptidase found among DPPs, mainly distributes within the cytoplasm. With the unique HEXXGH catalytic sequence, it is associated with the degradation of oligopeptides with 4 to 10 amino acids residues. Accumulating evidences have demonstrated that DPP3 plays a significant role in almost all cellular activities and pathophysiological mechanisms. Regarding the role of DPP3 in cardiovascular diseases, it is currently mainly used as a biomarker for poor prognosis in patients with cardiovascular diseases, suggesting that the level of DPP3 concentration in plasma is closely linked to the mortality of diseases such as cardiogenic shock and heart failure. Interestingly, it has been reported recently that DPP3 regulates blood pressure by interacting with the renin-angiotensin system. In addition, DPP3 also participates in the processes of pain signaling, inflammation, and oxidative stress. But the exact mechanism by which DPP3 affects cardiovascular function is not clear. Hence, this review summarizes the recent advances in the structure and catalytic activity of DPP3 and its extensive biological functions, especially its role as a therapeutic target in cardiovascular diseases. It will provide a theoretical basis for exploring the potential value of DPP3 as a therapeutic target for cardiovascular diseases.
Collapse
Affiliation(s)
- Peng Ye
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Duan
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,Key Laboratory of Medical Electrophysiology of Ministry of Education, Medical Electrophysiology Key Lab of Sichuan Province, Institute of Cardiovascular Research, Southwest Medical University, Luzhou, China
| | - Yue-Qi Leng
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Yang-Kai Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xing Tan
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,Xing Tan
| | - Wei-Zhong Wang
- Department of Marine Biomedicine and Polar Medicine, Naval Medical Center, Naval Medical University (Second Military Medical University), Shanghai, China,*Correspondence: Wei-Zhong Wang
| |
Collapse
|
9
|
Karačić Z, Šupljika F, Tomić A, Brkljačić L, Paić AT, Ćehić M, Tomić S. Neuropeptides, substrates and inhibitors of human dipeptidyl peptidase III, experimental and computational study - A new substrate identified. Int J Biol Macromol 2022; 220:1390-1401. [PMID: 36116590 DOI: 10.1016/j.ijbiomac.2022.09.119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022]
Abstract
Dipeptidyl peptidase III (DPP III) is a cytosolic, two-domain zinc-exopeptidase. It is widely distributed in mammalian tissues, where it's involved in the final steps of normal intracellular protein degradation. However, its pronounced affinity for some bioactive peptides (angiotensins, enkephalins, and endomorphins) suggests more specific functions such as blood pressure regulation and involvement in pain regulation. We have investigated several different neuropeptides as potential substrates and inhibitors of human DPP III. The binding affinities and kinetic data determined by isothermal titration calorimetry, in combination with measurements of enzyme inhibition identified the hemorphin-related valorphin, tynorphin, S-tynorphin, and I-tynorphin as the most potent inhibitors of DPP III (actually slow substrates), whereas hemorphin-4 proved to be the best substrate of all neuropeptides examined. In addition, we have shown that the neuropeptides valorphin, Leu-valorphin-Arg, and the opioid peptide β-casomorphin, are DPP III substrates. The molecular modelling of selected peptides shows uniform binding to the lower domain β-strand residues of DPP III via peptide backbone atoms, but also previously unrecognized stabilizing interactions with conserved residues of the metal-binding site and catalytic machinery in the upper domain. The computational data helped explain the differences between substrates that are hydrolyzed effectively and those hydrolysed slowly by DPP III.
Collapse
Affiliation(s)
- Zrinka Karačić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Filip Šupljika
- Faculty of Food Technology and Biotechnology, Department of Chemistry and Biochemistry, Pierottijeva 6, 10000 Zagreb, Croatia.
| | - Antonija Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Lidija Brkljačić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Ana Tomašić Paić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Mirsada Ćehić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Sanja Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Bijenička cesta 54, 10000 Zagreb, Croatia.
| |
Collapse
|
10
|
Podversnik H, Jha S, Macheroux P, Breinbauer R. Design and synthesis of efficient fluororethylene-peptidomimetic inhibitors of dipeptidyl peptidase III (DPP3). Bioorg Med Chem 2022; 67:116831. [PMID: 35623134 DOI: 10.1016/j.bmc.2022.116831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/02/2022]
Abstract
Dipeptidyl peptidase III (DPP3) is a ubiquitously expressed zinc-dependent peptide cutting enzyme and selectively hydrolyses amide bonds to cleave N-terminal dipeptide fragments off of physiologically important oligopeptides. DPP3 has been found in a multitude of different types of cells and appears to be involved in various physiological processes (e.g. nociception, blood pressure control, protein turnover). Using the slowly converted peptide substrate tynorphin (VVYPW) as starting point, we have replaced the scissile bond with a fluoroethylene bioisostere to design ground state inhibitors, which led to the so far most effective peptide-based inhibitor of DPP3.
Collapse
Affiliation(s)
- Harald Podversnik
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Petersgasse 10-12, A-8010 Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Petersgasse 10-12, A-8010 Graz, Austria; BIOTECHMED, Graz A-8010, Austria
| | - Rolf Breinbauer
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria; BIOTECHMED, Graz A-8010, Austria.
| |
Collapse
|
11
|
Landskron L, Bak J, Adamopoulos A, Kaplani K, Moraiti M, van den Hengel LG, Song JY, Bleijerveld OB, Nieuwenhuis J, Heidebrecht T, Henneman L, Moutin MJ, Barisic M, Taraviras S, Perrakis A, Brummelkamp TR. Posttranslational modification of microtubules by the MATCAP detyrosinase. Science 2022; 376:eabn6020. [PMID: 35482892 DOI: 10.1126/science.abn6020] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The detyrosination-tyrosination cycle involves the removal and religation of the C-terminal tyrosine of α-tubulin and is implicated in cognitive, cardiac, and mitotic defects. The vasohibin-small vasohibin-binding protein (SVBP) complex underlies much, but not all, detyrosination. We used haploid genetic screens to identify an unannotated protein, microtubule associated tyrosine carboxypeptidase (MATCAP), as a remaining detyrosinating enzyme. X-ray crystallography and cryo-electron microscopy structures established MATCAP's cleaving mechanism, substrate specificity, and microtubule recognition. Paradoxically, whereas abrogation of tyrosine religation is lethal in mice, codeletion of MATCAP and SVBP is not. Although viable, defective detyrosination caused microcephaly, associated with proliferative defects during neurogenesis, and abnormal behavior. Thus, MATCAP is a missing component of the detyrosination-tyrosination cycle, revealing the importance of this modification in brain formation.
Collapse
Affiliation(s)
- Lisa Landskron
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Jitske Bak
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Athanassios Adamopoulos
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Konstantina Kaplani
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Maria Moraiti
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Lisa G van den Hengel
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Ji-Ying Song
- Experimental Animal Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Onno B Bleijerveld
- Proteomics Facility, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Joppe Nieuwenhuis
- Division of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066CX Amsterdam, Netherlands
| | - Tatjana Heidebrecht
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Linda Henneman
- Transgenic Core Facility, Mouse Clinic for Cancer and Aging (MCCA), Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Marie-Jo Moutin
- Université Grenoble Alpes, INSERM, U1216, CNRS, Grenoble Institut Neurosciences, 38000 Grenoble, France
| | - Marin Barisic
- Cell Division and Cytoskeleton, Danish Cancer Society Research Center (DCRC), 2100 Copenhagen, Denmark.,Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stavros Taraviras
- Department of Physiology, School of Medicine, University of Patras, 26504 Patras, Greece
| | - Anastassis Perrakis
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| | - Thijn R Brummelkamp
- Oncode Institute, Division of Biochemistry, Netherlands Cancer Institute, 1066CX Amsterdam, Netherlands
| |
Collapse
|
12
|
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.
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Tomić A, Tomić S. Demystifying DPP III Catalyzed Peptide Hydrolysis—Computational Study of the Complete Catalytic Cycle of Human DPP III Catalyzed Tynorphin Hydrolysis. Int J Mol Sci 2022; 23:ijms23031858. [PMID: 35163780 PMCID: PMC8836397 DOI: 10.3390/ijms23031858] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/28/2022] [Accepted: 02/03/2022] [Indexed: 12/04/2022] Open
Abstract
Dipeptidyl peptides III (DPP III) is a dual-domain zinc exopeptidase that hydrolyzes peptides of varying sequence and size. Despite attempts to elucidate and narrow down the broad substrate-specificity of DPP III, there is no explanation as to why some of them, such as tynorphin (VVYPW), the truncated form of the endogenous heptapeptide spinorphin, are the slow-reacting substrates of DPP III compared to others, such as Leu-enkephalin. Using quantum molecular mechanics calculations followed by various molecular dynamics techniques, we describe for the first time the entire catalytic cycle of human DPP III, providing theoretical insight into the inhibitory mechanism of tynorphin. The chemical step of peptide bond hydrolysis and the substrate binding to the active site of the enzyme and release of the product were described for DPP III in complex with tynorphin and Leu-enkephalin and their products. We found that tynorphin is cleaved by the same reaction mechanism determined for Leu-enkephalin. More importantly, we showed that the product stabilization and regeneration of the enzyme, but not the nucleophilic attack of the catalytic water molecule and inversion at the nitrogen atom of the cleavable peptide bond, correspond to the rate-determining steps of the overall catalytic cycle of the enzyme.
Collapse
|
15
|
Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates. Molecules 2021; 26:molecules26216492. [PMID: 34770898 PMCID: PMC8587566 DOI: 10.3390/molecules26216492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 01/14/2023] Open
Abstract
Human dipeptidyl-peptidase III (hDPP III) is capable of specifically cleaving dipeptides from the N-terminal of small peptides with biological activity such as angiotensin II (Ang II, DRVYIHPF), and participates in blood pressure regulation, pain modulation, and the development of cancers in human biological activities. In this study, 500 ns molecular dynamics simulations were performed on free-hDPP III (PDB code: 5E33), hDPP III-Ang II (PDB code: 5E2Q), and hDPP III-IVYPW (PDB code: 5E3C) to explore how these two peptides affect the catalytic efficiency of enzymes in terms of the binding mode and the conformational changes. Our results indicate that in the case of the hDPP III-Ang II complex, subsite S1 became small and hydrophobic, which might be propitious for the nucleophile to attack the substrate. The structures of the most stable conformations of the three systems revealed that Arg421-Lys423 could form an α-helix with the presence of Ang II, but only part of the α-helix was produced in hDPP III-IVYPW. As the hinge structure in hDPP III, the conformational changes that took place in the Arg421-Lys423 residue could lead to the changes in the shape and space of the catalytic subsites, which might allow water to function as a nucleophile to attack the substrate. Our results may provide new clues to enable the design of new inhibitors for hDPP III in the future.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
Agić D, Karnaš M, Šubarić D, Lončarić M, Tomić S, Karačić Z, Bešlo D, Rastija V, Molnar M, Popović BM, Lisjak M. Coumarin Derivatives Act as Novel Inhibitors of Human Dipeptidyl Peptidase III: Combined In Vitro and In Silico Study. Pharmaceuticals (Basel) 2021; 14:ph14060540. [PMID: 34198854 PMCID: PMC8229952 DOI: 10.3390/ph14060540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 01/19/2023] Open
Abstract
Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is a member of the metalloproteinase family M49 with distribution detected in almost all forms of life. Although the physiological role of human DPP III (hDPP III) is not yet fully elucidated, its involvement in pathophysiological processes such as mammalian pain modulation, blood pressure regulation, and cancer processes, underscores the need to find new hDPP III inhibitors. In this research, five series of structurally different coumarin derivatives were studied to provide a relationship between their inhibitory profile toward hDPP III combining an in vitro assay with an in silico molecular modeling study. The experimental results showed that 26 of the 40 tested compounds exhibited hDPP III inhibitory activity at a concentration of 10 µM. Compound 12 (3-benzoyl-7-hydroxy-2H-chromen-2-one) proved to be the most potent inhibitor with IC50 value of 1.10 μM. QSAR modeling indicates that the presence of larger substituents with double and triple bonds and aromatic hydroxyl groups on coumarin derivatives increases their inhibitory activity. Docking predicts that 12 binds to the region of inter-domain cleft of hDPP III while binding mode analysis obtained by MD simulations revealed the importance of 7-OH group on the coumarin core as well as enzyme residues Ile315, Ser317, Glu329, Phe381, Pro387, and Ile390 for the mechanism of the binding pattern and compound 12 stabilization. The present investigation, for the first time, provides an insight into the inhibitory effect of coumarin derivatives on this human metalloproteinase.
Collapse
Affiliation(s)
- Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
- Correspondence:
| | - Maja Karnaš
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
| | - Domagoj Šubarić
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
| | - Melita Lončarić
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.L.); (M.M.)
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (S.T.); (Z.K.)
| | - Zrinka Karačić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (S.T.); (Z.K.)
| | - Drago Bešlo
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
| | - Vesna Rastija
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
| | - Maja Molnar
- Faculty of Food Technology Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.L.); (M.M.)
| | - Boris M. Popović
- Department of Field and Vegetable Crops, Faculty of Agriculture, University of Novi Sad, 21000 Novi Sad, Serbia;
| | - Miroslav Lisjak
- Faculty of Agrobiotechnical Sciences Osijek, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia; (M.K.); (D.Š.); (D.B.); (V.R.); (M.L.)
| |
Collapse
|
18
|
van Lier D, Kox M, Pickkers P. Promotion of vascular integrity in sepsis through modulation of bioactive adrenomedullin and dipeptidyl peptidase 3. J Intern Med 2021; 289:792-806. [PMID: 33381880 PMCID: PMC8246835 DOI: 10.1111/joim.13220] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/07/2020] [Accepted: 11/10/2020] [Indexed: 12/19/2022]
Abstract
Sepsis represents one of the major medical challenges of the 21st century. Despite substantial improvements in the knowledge on pathophysiological mechanisms, this has so far not translated into novel adjuvant treatment strategies for sepsis. In sepsis, both vascular tone and vascular integrity are compromised, and contribute to the development of shock, which is strongly related to the development of organ dysfunction and mortality. In this review, we focus on dipeptidyl peptidase 3 (DPP3) and adrenomedullin (ADM), two molecules that act on the vasculature and are involved in the pathophysiology of sepsis and septic shock. DPP3 is an ubiquitous cytosolic enzyme involved in the degradation of several important signalling molecules essential for regulation of vascular tone, including angiotensin II. ADM is a key hormone involved in the regulation of vascular tone and endothelial barrier function. Previous studies have shown that circulating concentrations of both DPP3 and ADM are independently associated with the development of organ failure and adverse outcome in sepsis. We now discuss new evidence illustrating that these molecules indeed represent two distinct pathways involved in the development of septic shock. Recently, both ADM-enhancing therapies aimed at improving endothelial barrier function and vascular tone and DPP3-blocking therapies aimed at restoring systemic angiotensin responses have been shown to improve outcome in various preclinical sepsis models. Given the current lack of effective adjuvant therapies in sepsis, additional research on the therapeutic application of these peptides in humans is highly warranted.
Collapse
Affiliation(s)
- D van Lier
- From the, Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - M Kox
- From the, Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - P Pickkers
- From the, Department of Intensive Care Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| |
Collapse
|
19
|
Appiah-Kubi P, Olotu FA, Soliman MES. Exploring the structural basis and atomistic binding mechanistic of the selective antagonist blockade at D 3 dopamine receptor over D 2 dopamine receptor. J Mol Recognit 2021; 34:e2885. [PMID: 33401335 DOI: 10.1002/jmr.2885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/17/2020] [Accepted: 12/15/2020] [Indexed: 12/28/2022]
Abstract
More recently, there has been a paradigm shift toward selective drug targeting in the treatment of neurological disorders, including drug addiction, schizophrenia, and Parkinson's disease mediated by the different dopamine receptor subtypes. Antagonists with higher selectivity for D3 dopamine receptor (D3DR) over D2 dopamine receptor (D2DR) have been shown to attenuate drug-seeking behavior and associated side effects compared to non-subtype selective antagonists. However, high conservations among constituent residues of both proteins, particularly at the ligand-binding pockets, remain a challenge to therapeutic drug design. Recent studies have reported the discovery of two small-molecules R-VK4-40 and Y-QA31 which substantially inhibited D3DR with >180-fold selectivity over D2DR. Therefore, in this study, we seek to provide molecular and structural insights into these differential binding mechanistic using meta-analytic computational simulation methods. Findings revealed that R-VK4-40 and Y-QA31 adopted shallow binding modes and were more surface-exposed at D3DR while on the contrary, they exhibited deep hydrophobic pocket binding at D2DR. Also, two non-conserved residues; Tyr361.39 and Ser18245.51 were identified in D3DR, based on their crucial roles and contributions to the selective binding of R-VK4-40 and Y-QA31. Importantly, both antagonists exhibited high affinities in complex with D3DR compared to D2DR, while van der Waals energies contributed majorly to their binding and stability. Structural analyses also revealed the distinct stabilizing effects of both compounds on D3DR secondary architecture relative to D2DR. Therefore, findings herein pinpointed the origin and mechanistic of selectivity of the compounds, which may assist in the rational design of potential small molecules of the D2 -like dopamine family receptor subtype with improved potency and selectivity.
Collapse
Affiliation(s)
- Patrick Appiah-Kubi
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Fisayo Andrew Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| |
Collapse
|
20
|
Matić S, Kekez I, Tomin M, Bogár F, Šupljika F, Kazazić S, Hanić M, Jha S, Brkić H, Bourgeois B, Madl T, Gruber K, Macheroux P, Matković-Čalogović D, Matovina M, Tomić S. Binding of dipeptidyl peptidase III to the oxidative stress cell sensor Kelch-like ECH-associated protein 1 is a two-step process. J Biomol Struct Dyn 2020; 39:6870-6881. [PMID: 32811353 DOI: 10.1080/07391102.2020.1804455] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
This work is about synergy of theory and experiment in revealing mechanism of binding of dipeptidyl peptidase III (DPP III) and Kelch-like ECH-associated protein 1 (KEAP1), the main cellular sensor of oxidative stress. The NRF2 ̶ KEAP1 signaling pathway is important for cell protection, but it is also impaired in many cancer cells where NRF2 target gene expression leads to resistance to chemotherapeutic drugs. DPP III competitively binds to KEAP1 in the conditions of oxidative stress and induces release of NRF2 and its translocation into nucleus. The binding is established mainly through the ETGE motif of DPP III and the Kelch domain of KEAP1. However, although part of a flexible loop, ETGE itself is firmly attached to the DPP III surface by strong hydrogen bonds. Using combined computational and experimental study, we found that DPP III ̶ Kelch binding is a two-step process comprising the endergonic loop detachment and exergonic DPP III ̶ Kelch interaction. Substitution of arginines, which keep the ETGE motif attached, decreases the work needed for its release and increases DPP III ̶ Kelch binding affinity. Interestingly, mutations of one of these arginine residues have been reported in cBioPortal for cancer genomics, implicating its possible involvement in cancer development. Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Sara Matić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ivana Kekez
- Department of Chemistry, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Marko Tomin
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ferenc Bogár
- Department of Medical Chemistry, MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Szeged, Hungary
| | - Filip Šupljika
- Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Saša Kazazić
- Divison of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Hanić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | - Hrvoje Brkić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia
| | - Benjamin Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & BiocBioTechMed-Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology & BiocBioTechMed-Graz, Graz, Austria.,BioTechMed-Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, Graz, Austria
| | | | - Mihaela Matovina
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Divison of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
21
|
Jha S, Taschler U, Domenig O, Poglitsch M, Bourgeois B, Pollheimer M, Pusch LM, Malovan G, Frank S, Madl T, Gruber K, Zimmermann R, Macheroux P. Dipeptidyl peptidase 3 modulates the renin-angiotensin system in mice. J Biol Chem 2020; 295:13711-13723. [PMID: 32546481 PMCID: PMC7535908 DOI: 10.1074/jbc.ra120.014183] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/12/2020] [Indexed: 12/12/2022] Open
Abstract
Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent hydrolase involved in degrading oligopeptides with 4-12 amino acid residues. It has been associated with several pathophysiological processes, including blood pressure regulation, pain signaling, and cancer cell defense against oxidative stress. However, the physiological substrates and the cellular pathways that are potentially targeted by DPP3 to mediate these effects remain unknown. Here, we show that global DPP3 deficiency in mice (DPP3-/-) affects the renin-angiotensin system (RAS). LC-MS-based profiling of circulating angiotensin peptides revealed elevated levels of angiotensin II, III, IV, and 1-5 in DPP3-/- mice, whereas blood pressure, renin activity, and aldosterone levels remained unchanged. Activity assays using the purified enzyme confirmed that angiotensin peptides are substrates for DPP3. Aberrant angiotensin signaling was associated with substantially higher water intake and increased renal reactive oxygen species formation in the kidneys of DPP3-/- mice. The metabolic changes and altered angiotensin levels observed in male DPP3-/- mice were either absent or attenuated in female DPP3-/- mice, indicating sex-specific differences. Taken together, our observations suggest that DPP3 regulates the RAS pathway and water homeostasis by degrading circulating angiotensin peptides.
Collapse
Affiliation(s)
- Shalinee Jha
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Ulrike Taschler
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria
| | | | | | - Benjamin Bourgeois
- Gottfried Schatz Research Center, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Marion Pollheimer
- Diagnostic & Research Institute of Pathology, Medical University of Graz, Graz, Austria
| | - Lisa M Pusch
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria
| | - Grazia Malovan
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria
| | - Saša Frank
- Gottfried Schatz Research Center, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Tobias Madl
- Gottfried Schatz Research Center, Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Karl Gruber
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria
| | - Robert Zimmermann
- Institute of Molecular Biosciences, University of Graz, NAWI Graz, Graz, Austria; BioTechMed Graz, Graz, Austria
| | - Peter Macheroux
- Institute of Biochemistry, Graz University of Technology, NAWI Graz, Graz, Austria.
| |
Collapse
|
22
|
Brulet JW, Borne AL, Yuan K, Libby AH, Hsu KL. Liganding Functional Tyrosine Sites on Proteins Using Sulfur-Triazole Exchange Chemistry. J Am Chem Soc 2020; 142:8270-8280. [PMID: 32329615 DOI: 10.1021/jacs.0c00648] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Tuning reactivity of sulfur electrophiles is key for advancing click chemistry and chemical probe discovery. To date, activation of the sulfur electrophile for protein modification has been ascribed principally to stabilization of a fluoride leaving group (LG) in covalent reactions of sulfonyl fluorides and arylfluorosulfates. We recently introduced sulfur-triazole exchange (SuTEx) chemistry to demonstrate the triazole as an effective LG for activating nucleophilic substitution reactions on tyrosine sites of proteins. Here, we probed tunability of SuTEx for fragment-based ligand discovery by modifying the adduct group (AG) and LG with functional groups of differing electron-donating and -withdrawing properties. We discovered the sulfur electrophile is highly sensitive to the position of modification (AG versus LG), which enabled both coarse and fine adjustments in solution and proteome activity. We applied these reactivity principles to identify a large fraction of tyrosine sites (∼30%) on proteins (∼44%) that can be liganded across >1500 probe-modified sites quantified by chemical proteomics. Our proteomic studies identified noncatalytic tyrosine and phosphotyrosine sites that can be liganded by SuTEx fragments with site specificity in lysates and live cells to disrupt protein function. Collectively, we describe SuTEx as a versatile covalent chemistry with broad applications for chemical proteomics and protein ligand discovery.
Collapse
Affiliation(s)
- Jeffrey W Brulet
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam L Borne
- Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States
| | - Kun Yuan
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Adam H Libby
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,University of Virginia Cancer Center, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Ku-Lung Hsu
- Department of Chemistry, University of Virginia, Charlottesville, Virginia 22904, United States.,Department of Pharmacology, University of Virginia School of Medicine, Charlottesville, Virginia 22908, United States.,University of Virginia Cancer Center, University of Virginia, Charlottesville, Virginia 22903, United States.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia 22908, United States
| |
Collapse
|
23
|
Tomić A, Horvat G, Ramek M, Agić D, Brkić H, Tomić S. New Zinc Ion Parameters Suitable for Classical MD Simulations of Zinc Metallopeptidases. J Chem Inf Model 2019; 59:3437-3453. [PMID: 31274304 DOI: 10.1021/acs.jcim.9b00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The main aim of this work was to find parameters for the zinc ion in human dipeptidyl peptidase III (DPP III) active site that would enable its reliable modeling. Since the parameters publicly available failed to reproduce the zinc ion coordination in the enzyme, we developed a new set of the hybrid bonded/nonbonded parameters for the zinc ion suitable for molecular modeling of the human DPP III, dynamics, and ligand binding. The parameters allowed exchange of the water molecules coordinating the zinc ion and proved to be robust enough to enable reliable modeling not only of human DPP III and its orthologues but also of the other zinc-dependent peptidases with the zinc ion coordination similar to that in dipeptidyl peptidases III, i.e., peptidases with the zinc ion coordinated with two histidines and one glutamate. The new parameters were tested on a set of 21 different systems comprising 8 different peptidases, 5 DPP III orthologues, thermolysin, neprilysin, and aminopeptidase N, and the results are summarized in the second part of the article.
Collapse
Affiliation(s)
- Antonija Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia.,Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science , University of Zagreb , Horvatovac 102A , 10 000 Zagreb , Croatia
| | - Michael Ramek
- Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , 8010 Graz , Austria
| | - Dejan Agić
- Faculty of Agrobiotechnical Sciences Osijek , Josip Juraj Strossmayer University of Osijek , Petra Svačića 1d , 31 000 Osijek , Croatia
| | - Hrvoje Brkić
- Faculty of Medicine , Josip Juraj Strossmayer University of Osijek , J. Huttlera 4 , 31 000 Osijek , Croatia.,Faculty of Dental Medicine and Health , Josip Juraj Strossmayer University of Osijek , Crkvena 21 , 31 000 Osijek , Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry , Ruđer Bošković Institute , Bijenička 54 , 10 000 Zagreb , Croatia
| |
Collapse
|
24
|
Tomin M, Tomić S. Oxidase or peptidase? A computational insight into a putative aflatoxin oxidase from Armillariella tabescens. Proteins 2019; 87:390-400. [PMID: 30681192 DOI: 10.1002/prot.25661] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Revised: 01/04/2019] [Accepted: 01/22/2019] [Indexed: 01/05/2023]
Abstract
Aflatoxin oxidase (AFO), an enzyme isolated from Armillariella tabescens, has been reported to degrade aflatoxin B1 (AFB1). However, recent studies reported sequence and structure similarities with the dipeptidyl peptidase III (DPP III) family of enzymes and confirmed peptidase activity toward DPP III substrates. In light of these investigations, an extensive computational study was performed in order to improve understanding of the AFO functions. Steered MD simulations revealed long-range domain motions described as protein opening, characteristic for DPPs III and necessary for substrate binding. Newly identified open and partially open forms of the enzyme closely resemble those of the human DPP III orthologue. Docking of a synthetic DPP III substrate Arg2 -2-naphthylamide revealed a binding mode similar to the one found in crystal structures of human DPP III complexes with peptides with the S1 and S2 subsites' amino acid residues conserved. On the other hand, no energetically favorable AFB1 binding mode was detected, suggesting that aflatoxins are not good substrates of AFO. High plasticity of the zinc ion coordination sphere within the active site, consistent with that of up to date studied DPPs III, was observed as well. A detailed electrostatic analysis of the active site revealed a predominance of negatively charged regions, unsuitable for the binding of the neutral AFB1. The present study is in line with the most recent experimental study on this enzyme, both suggesting that AFO is a typical member of the DPP III family.
Collapse
Affiliation(s)
- Marko Tomin
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| |
Collapse
|
25
|
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
| |
Collapse
|
26
|
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.
Collapse
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:
| |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Dipeptidyl peptidase 3, a novel protease from Leishmania braziliensis. PLoS One 2018; 13:e0190618. [PMID: 29304092 PMCID: PMC5755878 DOI: 10.1371/journal.pone.0190618] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 12/18/2017] [Indexed: 12/13/2022] Open
Abstract
The increase of leishmaniasis cases worldwide and the emergence of Leishmania strains resistant to current treatments make necessary to find new therapeutic targets. Proteases are appealing drug targets because they play pivotal roles in facilitating parasite survival and promoting pathogenesis. Enzymes belonging to the dipeptidyl peptidase 3 (DPP3) group have been described in different organisms such as mammals, insects and yeast, in which these enzymes have been involved in both protein turnover and protection against oxidative damage. The aim of this work was to characterize the structure and function of the Leishmania braziliensis DPP3 (LbDPP3) protein as the first step to elucidate its suitability as a potential drug target. Sequence alignment showed 43% of identity between LbDPP3 and its human orthologous (hDPP3) enzyme. Although the modeled protein adopted a globally conserved three-dimensional (3D) structure, structural differences were found in the vicinity of the active site and the substrate binding-cleft. In addition, the Leishmania protein was expressed as a soluble recombinant protein and its kinetics parameters were determined using the z-Arginine-Arginine-AMC substrate. The LbDPP3 activity was maximal at pH values between 8.0–8.5. Interestingly, classical enzyme inhibitors such as the tynorphin and its derivative peptide IVYPW were found to actively inhibit the LbDPP3 activity. Moreover, these DPP3 inhibitors showed a detrimental effect upon parasite survival, decreasing the viability of promastigotes by up to 29%. Finally, it was observed that LbDPP3 was equally expressed along the in vitro differentiation from promastigotes to axenic amastigotes. In conclusion, these findings suggest that the L. brazileinsis DPP3 could be a promising drug target.
Collapse
|
29
|
Kazazić S, Karačić Z, Sabljić I, Agić D, Tomin M, Abramić M, Dadlez M, Tomić A, Tomić S. Conservation of the conformational dynamics and ligand binding within M49 enzyme family. RSC Adv 2018; 8:13310-13322. [PMID: 35542530 PMCID: PMC9079729 DOI: 10.1039/c7ra13059g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 03/28/2018] [Indexed: 12/25/2022] Open
Abstract
The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family). Six dipeptidyl peptidase III (DPP III) orthologues, human, yeast, three bacterial and one plant (moss) were studied. According to the results, all orthologues seem to be quite compact wherein DPP III from the thermophile Caldithrix abyssi seems to be the most compact. The protected regions are located within the two domains core and the overall flexibility profile consistent with semi-closed conformation as the dominant protein form in solution. Besides conservation of conformational dynamics within the M49 family, we also investigated the ligand, pentapeptide tynorphin, binding. By comparing HDX data obtained for unliganded protein with those obtained for its complex with tynorphin it was found that the ligand binding mode is conserved within the family. Tynorphin binds within inter-domain cleft, close to the lower domain β-core and induces its stabilization in all orthologues. Docking combined with MD simulations revealed details of the protein flexibility as well as of the enzyme–ligand interactions. The hydrogen deuterium exchange (HDX) mass spectrometry combined with molecular dynamics (MD) simulations was employed to investigate conformational dynamics and ligand binding within the M49 family (dipeptidyl peptidase III family).![]()
Collapse
Affiliation(s)
- Saša Kazazić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Zrinka Karačić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Igor Sabljić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Dejan Agić
- Josip Juraj Strossmayer University of Osijek
- Faculty of Agriculture
- Croatia
| | - Marko Tomin
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Marija Abramić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Michal Dadlez
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Poland
| | - Antonija Tomić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| | - Sanja Tomić
- Ruđer Bošković Institute
- Institute of Biochemistry and Biophysics Polish Academy of Sciences
- Croatia
| |
Collapse
|
30
|
Protein conformational flexibility modulates kinetics and thermodynamics of drug binding. Nat Commun 2017; 8:2276. [PMID: 29273709 PMCID: PMC5741624 DOI: 10.1038/s41467-017-02258-w] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/16/2017] [Indexed: 12/15/2022] Open
Abstract
Structure-based drug design has often been restricted by the rather static picture of protein-ligand complexes presented by crystal structures, despite the widely accepted importance of protein flexibility in biomolecular recognition. Here we report a detailed experimental and computational study of the drug target, human heat shock protein 90, to explore the contribution of protein dynamics to the binding thermodynamics and kinetics of drug-like compounds. We observe that their binding properties depend on whether the protein has a loop or a helical conformation in the binding site of the ligand-bound state. Compounds bound to the helical conformation display slow association and dissociation rates, high-affinity and high cellular efficacy, and predominantly entropically driven binding. An important entropic contribution comes from the greater flexibility of the helical relative to the loop conformation in the ligand-bound state. This unusual mechanism suggests increasing target flexibility in the bound state by ligand design as a new strategy for drug discovery.
Collapse
|
31
|
A novel Porphyromonas gingivalis enzyme: An atypical dipeptidyl peptidase III with an ARM repeat domain. PLoS One 2017; 12:e0188915. [PMID: 29190734 PMCID: PMC5708649 DOI: 10.1371/journal.pone.0188915] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/15/2017] [Indexed: 11/30/2022] Open
Abstract
Porphyromonas gingivalis, an asaccharolytic Gram-negative oral anaerobe, is a major pathogen associated with adult periodontitis, a chronic infective disease that a significant percentage of the human population suffers from. It preferentially utilizes dipeptides as its carbon source, suggesting the importance of dipeptidyl peptidase (DPP) types of enzyme for its growth. Until now DPP IV, DPP5, 7 and 11 have been extensively investigated. Here, we report the characterization of DPP III using molecular biology, biochemical, biophysical and computational chemistry methods. In addition to the expected evolutionarily conserved regions of all DPP III family members, PgDPP III possesses a C-terminal extension containing an Armadillo (ARM) type fold similar to the AlkD family of bacterial DNA glycosylases, implicating it in alkylation repair functions. However, complementation assays in a DNA repair-deficient Escherichia coli strain indicated the absence of alkylation repair function for PgDPP III. Biochemical analyses of recombinant PgDPP III revealed activity similar to that of DPP III from Bacteroides thetaiotaomicron, and in the range between activities of human and yeast counterparts. However, the catalytic efficiency of the separately expressed DPP III domain is ~1000-fold weaker. The structure and dynamics of the ligand-free enzyme and its complex with two different diarginyl arylamide substrates was investigated using small angle X-ray scattering, homology modeling, MD simulations and hydrogen/deuterium exchange (HDX). The correlation between the experimental HDX and MD data improved with simulation time, suggesting that the DPP III domain adopts a semi-closed or closed form in solution, similar to that reported for human DPP III. The obtained results reveal an atypical DPP III with increased structural complexity: its superhelical C-terminal domain contributes to peptidase activity and influences DPP III interdomain dynamics. Overall, this research reveals multifunctionality of PgDPP III and opens direction for future research of DPP III family proteins.
Collapse
|
32
|
Crystal structure of dipeptidyl peptidase III from the human gut symbiont Bacteroides thetaiotaomicron. PLoS One 2017; 12:e0187295. [PMID: 29095893 PMCID: PMC5667867 DOI: 10.1371/journal.pone.0187295] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 10/17/2017] [Indexed: 02/06/2023] Open
Abstract
Bacteroides thetaiotaomicron is a dominant member of the human intestinal microbiome. The genome of this anaerobe encodes more than 100 proteolytic enzymes, the majority of which have not been characterized. In the present study, we have produced and purified recombinant dipeptidyl peptidase III (DPP III) from B. thetaiotaomicron for the purposes of biochemical and structural investigations. DPP III is a cytosolic zinc-metallopeptidase of the M49 family, involved in protein metabolism. The biochemical results for B. thetaiotaomicron DPP III from our research showed both some similarities to, as well as certain differences from, previously characterised yeast and human DPP III. The 3D-structure of B. thetaiotaomicron DPP III was determined by X-ray crystallography and revealed a two-domain protein. The ligand-free structure (refined to 2.4 Å) was in the open conformation, while in the presence of the hydroxamate inhibitor Tyr-Phe-NHOH, the closed form (refined to 3.3 Å) was observed. Compared to the closed form, the two domains of the open form are rotated away from each other by about 28 degrees. A comparison of the crystal structure of B. thetaiotaomicron DPP III with that of the human and yeast enzymes revealed a similar overall fold. However, a significant difference with functional implications was discovered in the upper domain, farther away from the catalytic centre. In addition, our data indicate that large protein flexibility might be conserved in the M49 family.
Collapse
|
33
|
Crystal structures of Aflatoxin-oxidase from Armillariella tabescens reveal a dual activity enzyme. Biochem Biophys Res Commun 2017; 494:621-625. [PMID: 29050944 DOI: 10.1016/j.bbrc.2017.10.077] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 10/15/2017] [Indexed: 01/29/2023]
Abstract
Aflatoxin-oxidase (AFO), a newly discovered oxidase isolated from Armillariella tabescens, was reported to perform aflatoxin B1 (AFB1) detoxification through breaking the bisfuran ring of AFB1. However, based on sequence alignment, we found that AFO shares high sequence identities with dipeptidyl peptidase III (DPP III) family members. To understand the functions of AFO, we determined its crystal structures in the absence and presence of zinc, copper ion, and employed HPLC to test if AFO could cleave the substrates of DPP III. Our structures reveal that AFO contains the classic DPP III activity center and the HPLC results further confirm that AFO possesses the dipeptidyl peptidase activity. Therefore, AFO should belong to DPP III family. Interestingly, unlike reported classic DPP III structure that has a large domain movement upon substrate binding, the AFO structures all adopt the closed conformation, independent of substrate binding. This conformation characteristic of AFO may be related to its enzyme activities. Taken together, our results demonstrate that AFO is a dual activity enzyme with both aflatoxin-oxidase and dipeptidyl peptidase activities and its unique conformation feature expands our understanding on the mode of reaction for this enzyme family.
Collapse
|
34
|
Pinto G, Mazzone G, Russo N, Toscano M. Trimethylphosphate and Dimethylphosphate Hydrolysis by Binuclear CdII
, MnII
, and ZnII
-FeII
Promiscuous Organophosphate-Degrading Enzyme: Reaction Mechanisms. Chemistry 2017; 23:13742-13753. [DOI: 10.1002/chem.201702379] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Gaspar Pinto
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Gloria Mazzone
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Nino Russo
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| | - Marirosa Toscano
- Department Of Chemistry and Chemical Technologies; University of Calabria; Via P. Bucci 87036 Arcavacata di Rende Italy
| |
Collapse
|
35
|
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.
Collapse
|
36
|
Bacterial protease uses distinct thermodynamic signatures for substrate recognition. Sci Rep 2017; 7:2848. [PMID: 28588213 PMCID: PMC5460201 DOI: 10.1038/s41598-017-03220-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 05/02/2017] [Indexed: 12/30/2022] Open
Abstract
Porphyromonas gingivalis and Porphyromonas endodontalis are important bacteria related to periodontitis, the most common chronic inflammatory disease in humans worldwide. Its comorbidity with systemic diseases, such as type 2 diabetes, oral cancers and cardiovascular diseases, continues to generate considerable interest. Surprisingly, these two microorganisms do not ferment carbohydrates; rather they use proteinaceous substrates as carbon and energy sources. However, the underlying biochemical mechanisms of their energy metabolism remain unknown. Here, we show that dipeptidyl peptidase 11 (DPP11), a central metabolic enzyme in these bacteria, undergoes a conformational change upon peptide binding to distinguish substrates from end products. It binds substrates through an entropy-driven process and end products in an enthalpy-driven fashion. We show that increase in protein conformational entropy is the main-driving force for substrate binding via the unfolding of specific regions of the enzyme (“entropy reservoirs”). The relationship between our structural and thermodynamics data yields a distinct model for protein-protein interactions where protein conformational entropy modulates the binding free-energy. Further, our findings provide a framework for the structure-based design of specific DPP11 inhibitors.
Collapse
|
37
|
The Development of Translational Biomarkers as a Tool for Improving the Understanding, Diagnosis and Treatment of Chronic Neuropathic Pain. Mol Neurobiol 2017; 55:2420-2430. [PMID: 28361271 PMCID: PMC5840239 DOI: 10.1007/s12035-017-0492-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 03/14/2017] [Indexed: 12/13/2022]
Abstract
Chronic neuropathic pain (CNP) is one of the most significant unmet clinical needs in modern medicine. Alongside the lack of effective treatments, there is a great deficit in the availability of objective diagnostic methods to reliably facilitate an accurate diagnosis. We therefore aimed to determine the feasibility of a simple diagnostic test by analysing differentially expressed genes in the blood of patients diagnosed with CNP of the lower back and compared to healthy human controls. Refinement of microarray expression data was performed using correlation analysis with 3900 human 2-colour microarray experiments. Selected genes were analysed in the dorsal horn of Sprague-Dawley rats after L5 spinal nerve ligation (SNL), using qRT-PCR and ddPCR, to determine possible associations with pathophysiological mechanisms underpinning CNP and whether they represent translational biomarkers of CNP. We found that of the 15 potential biomarkers identified, tissue inhibitor of matrix metalloproteinase-1 (TIMP1) gene expression was upregulated in chronic neuropathic lower back pain (CNBP) (p = 0.0049) which positively correlated (R = 0.68, p = ≤0.05) with increased plasma TIMP1 levels in this group (p = 0.0433). Moreover, plasma TIMP1 was also significantly upregulated in CNBP than chronic inflammatory lower back pain (p = 0.0272). In the SNL model, upregulation of the Timp1 gene was also observed (p = 0.0058) alongside a strong trend for the upregulation of melanocortin 1 receptor (p = 0.0847). Our data therefore highlights several genes that warrant further investigation, and of these, TIMP1 shows the greatest potential as an accessible and translational CNP biomarker.
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
Agić D, Brkić H, Tomić S, Karačić Z, Špoljarević M, Lisjak M, Bešlo D, Abramić M. Validation of flavonoids as potential dipeptidyl peptidase III inhibitors: Experimental and computational approach. Chem Biol Drug Des 2016; 89:619-627. [DOI: 10.1111/cbdd.12887] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/05/2016] [Accepted: 10/08/2016] [Indexed: 10/20/2022]
Affiliation(s)
- Dejan Agić
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Hrvoje Brkić
- Faculty of Medicine; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | | | | | - Marija Špoljarević
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Miroslav Lisjak
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | - Drago Bešlo
- Faculty of Agriculture in Osijek; Josip Juraj Strossmayer University of Osijek; Osijek Croatia
| | | |
Collapse
|
42
|
Abdullatypov AV, Kondratyev MS, Holyavka MG, Artyukhov VG. Reconstruction of the spatial structure of inulinase from Kluyveromyces marxianus to find regulatory pathways of its catalytic activity. Biophysics (Nagoya-shi) 2016. [DOI: 10.1134/s0006350916040023] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
|
43
|
Tomić A, Berynskyy M, Wade RC, Tomić S. Molecular simulations reveal that the long range fluctuations of human DPP III change upon ligand binding. MOLECULAR BIOSYSTEMS 2016; 11:3068-80. [PMID: 26334575 DOI: 10.1039/c5mb00465a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The experimentally determined structures of human dipeptidyl peptidase III (DPP III) for the wild-type protein and for the complex of its E451A mutant with the peptide substrate, tynorphin, differ significantly in their overall shape. The two domains of the enzyme are separated by a wide cleft in the structure of the ligand-free enzyme, while in the ligand-bound mutant they are very close to each other, and the protein structure is extremely compact. Here, we applied a range of molecular dynamics simulation techniques to investigate the DPP III conformational landscape and the influence of ligand binding on the protein structure and dynamics. We used conventional, accelerated and steered methods to simulate DPP III and its complexes with tynorphin and with the preferred, synthetic, substrate Arg-Arg-2-naphthylamide. We found that DPP III can adopt a number of different forms in solution. The compact forms are more stable, but the open and partially closed states, spanning a wide range of conformations, can more effectively recognize the substrate which preferentially binds to the five-stranded β-core of the lower DPP III domain. The simulations indicated the existence of a dynamic equilibrium between open and semi-closed states and revealed two ways that the protein can close, leading to two distinct compact structures. The way in which the protein closes depends on the presence of the ligand.
Collapse
Affiliation(s)
- A Tomić
- Department of Physical Chemistry, Rudjer Boskovic Institute, Bijenička cesta 54, 10000, Zagreb, Croatia.
| | | | | | | |
Collapse
|
44
|
Pang X, Shimizu A, Kurita S, Zankov DP, Takeuchi K, Yasuda-Yamahara M, Kume S, Ishida T, Ogita H. Novel Therapeutic Role for Dipeptidyl Peptidase III in the Treatment of Hypertension. Hypertension 2016; 68:630-41. [PMID: 27456521 DOI: 10.1161/hypertensionaha.116.07357] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 05/26/2016] [Indexed: 01/10/2023]
Abstract
Dipeptidyl peptidase III (DPP III) cleaves dipeptide residues from the N terminus of polypeptides ranging from 3 to 10 amino acids in length and is implicated in pathophysiological processes through the breakdown of certain oligopeptides or their fragments. In this study, we newly identified the biochemical properties of DPP III for angiotensin II (Ang II), which consists of 8 amino acids. DPP III quickly and effectively digested Ang II with Km = 3.7×10(-6) mol/L. In the in vivo experiments, DPP III remarkably reduced blood pressure in Ang II-infused hypertensive mice without alteration of heart rate. DPP III did not affect hemodynamics in noradrenalin-induced hypertensive mice or normotensive mice, suggesting specificity for Ang II. When DPP III was intravenously injected every other day for 4 weeks after Ang II osmotic minipump implantation in mice, Ang II-induced cardiac fibrosis and hypertrophy were significantly attenuated. This DPP III effect was at least similar to that caused by an angiotensin receptor blocker candesartan. Furthermore, administration of DPP III dramatically reduced the increase in urine albumin excretion and kidney injury and inflammation markers caused by Ang II infusion. Both DPP III and candesartan administration showed slight additive inhibition in the albumin excretion. These results reveal a novel potential use of DPP III in the treatment of hypertension and its protective effects on hypertension-sensitive organs, such as the heart and kidneys.
Collapse
Affiliation(s)
- Xiaoling Pang
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Akio Shimizu
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Souichi Kurita
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Dimitar P Zankov
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Keisuke Takeuchi
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Mako Yasuda-Yamahara
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Shinji Kume
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Tetsuo Ishida
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.)
| | - Hisakazu Ogita
- From the Division of Molecular Medical Biochemistry, Department of Biochemistry and Molecular Biology (X.P., A.S., S.Kurita, D.P.Z., K.T., H.O.), Division of Diabetology, Endocrinology, Nephrology, and Neurology, Department of Medicine, Shiga University of Medical Science, Otsu, Japan (M.Y-Y., S.Kume); Chemistry Division, Department of Chemistry, Biology and Marine Science, Faculty of Science, University of the Ryukyus, Nishihara-cho, Japan (T.I.); and Department of Emergency, The Fourth Affiliated Hospital of China Medical University, Shenyang, China (X.P.).
| |
Collapse
|
45
|
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.
Collapse
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
| | | | | |
Collapse
|
46
|
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.
Collapse
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
| |
Collapse
|
47
|
Matić J, Šupljika F, Tir N, Piotrowski P, Schmuck C, Abramić M, Piantanida I, Tomić S. Guanidiniocarbonyl-pyrrole-aryl conjugates as inhibitors of human dipeptidyl peptidase III: combined experimental and computational study. RSC Adv 2016. [DOI: 10.1039/c6ra16966j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Good overlap of the standard DPP III substrate Arg-Arg-2NA (magenta) and the most efficient novel inhibitor (guanidiniocarbonyl-pyrrole-pyrene conjugate, blue-red) in the DPP III binding site.
Collapse
Affiliation(s)
- Josipa Matić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Filip Šupljika
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Nora Tir
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Carsten Schmuck
- Institute for Organic Chemistry
- University of Duisburg-Essen
- Universitässtrasse 7
- 45141 Essen
- Germany
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- 10000 Zagreb
- Croatia
| |
Collapse
|
48
|
Tomić A, Tomić S. Hunting the human DPP III active conformation: combined thermodynamic and QM/MM calculations. Dalton Trans 2015; 43:15503-14. [PMID: 25192149 DOI: 10.1039/c4dt02003k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple choices of the protein active conformations in flexible metalloenzymes complicate study of their catalytic mechanism. We used three different conformations of human dipeptidyl-peptidase III (DPP III) to investigate the influence of the protein environment on ligand binding and the Zn(2+) coordination. MD simulations followed by calculations of binding free energy components accomplished for a series of DPP III substrates, both synthetic and natural, revealed that binding of the β-strand shaped substrate to the five-stranded β-core of the compact DPP III form (in antiparallel fashion) is the preferred binding mode, in agreement with the experimentally determined structure of the DPP III inactive mutant-tynorphin complex (Bezerra et al., Proc. Natl. Acad. Sci. U. S. A., 2012, 109, 6525). Previously it was proposed that the catalytic mechanism of DPP III is similar to that of thermolysin, which assumes exchange of five and four coordinated Zn(2+), and activation of Zn-bound water by a nearby Glu. Our QM/MM calculations, performed for a total of 18 protein structures with different zinc ion environments, revealed that the 5-coordinated metal ion is more favourable than the 6-coordinated one in only the most compact DPP III form. Besides, in this structure E451 is H-bonded to the metal ion coordinating water. Also, our study revealed two constraints for the broad substrate specificity of DPP III. One is the possibility of the substrate adopting the β-strand shape and the other is its charged N-terminus. Altogether, we assume that the human DPP III active conformation would be the most compact form, similar to the "closed X-ray" DPP III structure.
Collapse
Affiliation(s)
- Antonija Tomić
- Division of Physical Chemistry, Ruđer Bošković Institute, Bijenička 54, 10 000 Zagreb, Croatia.
| | | |
Collapse
|
49
|
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.
Collapse
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
| |
Collapse
|
50
|
Singh R, Sharma MC, Sarkar C, Singh M, Chauhan SS. Transcription factor C/EBP-β mediates downregulation of dipeptidyl-peptidase III expression by interleukin-6 in human glioblastoma cells. FEBS J 2014; 281:1629-41. [PMID: 24472318 DOI: 10.1111/febs.12728] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/28/2013] [Accepted: 01/22/2014] [Indexed: 11/30/2022]
Abstract
Dipeptidyl-peptidase III (DPP III) is a cytosolic metallo-aminopeptidase implicated in various physiological and pathological processes. A previous study from our laboratory indicated an elevated expression of DPP III in glioblastoma (U87MG) cells. In the present study we investigated the role of interleukin-6 (IL-6), a pleiotropic cytokine produced by glial tumors, in the regulation of DPP III expression. Immunohistochemistry, western blotting and quantitative RT-PCR were used for quantitation of DPP III and IL-6 in human glioblastoma cells and tumors. Cell transfections and DPP III promoter reporter assays were performed to study the transcriptional regulation of DPP III by IL-6. Promoter deletion analysis, site directed mutagenesis, chromatin immunoprecipitation assays and small interfering RNA (siRNA) technology was employed to elucidate the molecular mechanism of IL-6 mediated regulation of DPP III expression in glioblastoma cells. Our results for the first time demonstrate a negative correlation (r = 0.632, P = 0.01) between DPP III and IL-6 in both human tumors and cultured glioblastoma cells. Treatment of U87MG cells with IL-6 significantly decreased DPP III expression with a concomitant increase in the levels of transcription factor CCAAT/enhancer binding protein beta (C/EBP-β). Deletion/mutagenesis of C/EBP-β binding motif of DPP III promoter significantly increased its activity and abolished its responsiveness to IL-6. This effect could also be mimicked by C/EBP-β siRNA. In conclusion our study for the first time demonstrates C/EBP-β mediated transcriptional downregulation of DPP III by IL-6. Our results demonstrating a negative correlation between IL-6 and DPP III taken together with the previously reported prognostic significance of this cytokine in glioblastoma suggests that DPP III may prove useful as a prognostic marker.
Collapse
Affiliation(s)
- Ratnakar Singh
- Department of Biochemistry, All India Institute of Medical Sciences, New Delhi, India
| | | | | | | | | |
Collapse
|