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Matovina M, Tomašić Paić A, Tomić S, Brkić H, Horvat L, Barbarić L, Filić V, Pinterić M, Jurić S, Kussayeva A. Identification of SH2 Domain-Containing Protein 3C as a Novel, Putative Interactor of Dipeptidyl Peptidase 3. Int J Mol Sci 2023; 24:14178. [PMID: 37762480 PMCID: PMC10532290 DOI: 10.3390/ijms241814178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Dipeptidyl peptidase 3 (DPP3) is a zinc-dependent exopeptidase with broad specificity for four to eight amino acid residue substrates. It has a role in the regulation of oxidative stress response NRF2-KEAP1 pathway through the interaction with KEAP1. We have conducted stable isotope labeling by amino acids in a cell culture coupled to mass spectrometry (SILAC-MS) interactome analysis of TRex HEK293T cells using DPP3 as bait and identified SH2 Domain-Containing Protein 3C (SH2D3C) as prey. SH2D3C is one of three members of a family of proteins that contain both the SH2 domain and a domain similar to guanine nucleotide exchange factor domains of Ras family GTPases (Ras GEF-like domain), named novel SH2-containing proteins (NSP). NSPs, including SH2D3C (NSP3), are adaptor proteins involved in the regulation of adhesion, migration, tissue organization, and immune response. We have shown that SH2D3C binds to DPP3 through its C-terminal Ras GEF-like domain, detected the colocalization of the proteins in living cells, and confirmed direct interaction in the cytosol and membrane ruffles. Computational analysis also confirmed the binding of the C-terminal domain of SH2D3C to DPP3, but the exact model could not be discerned. This is the first indication that DPP3 and SH2D3C are interacting partners, and further studies to elucidate the physiological significance of this interaction are on the way.
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Affiliation(s)
- Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Hrvoje Brkić
- Faculty of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia;
| | - Lucija Horvat
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.H.); (V.F.)
| | - Lea Barbarić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Vedrana Filić
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.H.); (V.F.)
| | - Marija Pinterić
- Division of Molecular Medicine, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia;
| | - Snježana Jurić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
| | - Akmaral Kussayeva
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (A.T.P.); (S.T.); (L.B.); (S.J.); (A.K.)
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2
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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.
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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
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3
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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.
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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.
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4
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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.
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5
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Tomić A, Brkić H, Matić A, Tomić S. Unravelling the inhibitory zinc ion binding site and the metal exchange mechanism in human DPP III. Phys Chem Chem Phys 2021; 23:13267-13275. [PMID: 34095907 DOI: 10.1039/d1cp01302e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Dipeptidyl peptidase III (DPP III), a zinc-dependent exopeptidase, is widely distributed in organisms and present in almost all human tissues. In addition to its involvement in protein catabolism, it plays a role in oxidative stress and blood pressure regulation, and there is evidence of its involvement in pain modulation. Excess zinc ions have been found to inhibit its hydrolytic activity, but the binding affinity, binding site geometry, and mechanism of inhibitory activity have been unknown. Using several different computational approaches, we determined the inhibitory zinc ion binding site, its coordination and relative binding affinity. During some simulations the translocation of the zinc ion from the inhibitory to the catalytic binding site was observed, accompanied by movement of the catalytic zinc ion toward the exit of the substrate binding site. The traced behavior suggests an associative type of metal ion exchange, in which the formation of the ternary complex between enzyme and two metal ions precedes the exit of the catalytic metal ion. Differently from our previous findings that binding of a peptide induces partial opening of hDPP III, the globularity of the protein did not change in MD simulations of the hermorphin-like peptide bound to hDPP III with two zinc ions. However, the entrance to the interdomain cleft widens during Zn diffusion into the protein and was found to be the highest energy barrier in the process of metal translocation from the solvent to the active site. Finally, we discuss why excess zinc reduces enzyme activity.
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Affiliation(s)
- Antonija Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Croatia.
| | - Hrvoje Brkić
- J. J. Strossmayer University of Osijek, Faculty of Medicine, Croatia and J. J. Strossmayer University of Osijek, Faculty of Dental Medicine and Health, Croatia
| | - Antonia Matić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Croatia.
| | - Sanja Tomić
- Ruđer Bošković Institute, Division of Organic Chemistry and Biochemistry, Croatia.
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6
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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.
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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.)
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7
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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.
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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
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Pinto GP, Vavra O, Filipovic J, Stourac J, Bednar D, Damborsky J. Fast Screening of Inhibitor Binding/Unbinding Using Novel Software Tool CaverDock. Front Chem 2019; 7:709. [PMID: 31737596 PMCID: PMC6828983 DOI: 10.3389/fchem.2019.00709] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Accepted: 10/09/2019] [Indexed: 11/20/2022] Open
Abstract
Protein tunnels and channels are attractive targets for drug design. Drug molecules that block the access of substrates or release of products can be efficient modulators of biological activity. Here, we demonstrate the applicability of a newly developed software tool CaverDock for screening databases of drugs against pharmacologically relevant targets. First, we evaluated the effect of rigid and flexible side chains on sets of substrates and inhibitors of seven different proteins. In order to assess the accuracy of our software, we compared the results obtained from CaverDock calculation with experimental data previously collected with heat shock protein 90α. Finally, we tested the virtual screening capabilities of CaverDock with a set of oncological and anti-inflammatory FDA-approved drugs with two molecular targets—cytochrome P450 17A1 and leukotriene A4 hydrolase/aminopeptidase. Calculation of rigid trajectories using four processors took on average 53 min per molecule with 90% successfully calculated cases. The screening identified functional tunnels based on the profile of potential energies of binding and unbinding trajectories. We concluded that CaverDock is a sufficiently fast, robust, and accurate tool for screening binding/unbinding processes of pharmacologically important targets with buried functional sites. The standalone version of CaverDock is available freely at https://loschmidt.chemi.muni.cz/caverdock/ and the web version at https://loschmidt.chemi.muni.cz/caverweb/.
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Affiliation(s)
- Gaspar P Pinto
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Ondrej Vavra
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jiri Filipovic
- Institute of Computer Science, Masaryk University, Brno, Czechia
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czechia.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czechia
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9
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Ćehić M, Suć Sajko J, Karačić Z, Piotrowski P, Šmidlehner T, Jerić I, Schmuck C, Piantanida I, Tomić S. The guanidiniocarbonylpyrrole-fluorophore conjugates as theragnostic tools for dipeptidyl peptidase III monitoring and inhibition. J Biomol Struct Dyn 2019; 38:3790-3800. [PMID: 31496375 DOI: 10.1080/07391102.2019.1664936] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Study of seven new guanidiniocarbonylpyrrole (GCP)-fluorophore conjugates interactions with dipeptidyl peptidase III (DPP III) showed that all compounds bind strongly (Ks ≈ µM) to enzyme active site, but with very different fluorimetric response (varying from quenching to strong increase), dependent on the fluorophore type and intramolecular pre-organisation of molecule. Positively charged lysine side chain improved significantly compound solubility but diminished fluorescence increase upon DPP III binding and completely abolished inhibitory effect on DPP III activity, whereas linker-neutral analogues showed stronger emission increase and were efficient enzyme inhibitors. By far the best fluorimetric response and inhibitive properties showed cyanine-GCP analogue, thus being promising lead compound for both enzyme sensing and bio-activity inhibiting (theragnostic) studies of DPP III in the future.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | | | - Carsten Schmuck
- Institute of Organic Chemistry, University of Duisburg-Essen, Essen, Germany
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10
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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.
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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
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11
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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.
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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
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12
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Sabljić I, Tomin M, Matovina M, Sučec I, Tomašić Paić A, Tomić A, Abramić M, Tomić S. The first dipeptidyl peptidase III from a thermophile: Structural basis for thermal stability and reduced activity. PLoS One 2018; 13:e0192488. [PMID: 29420664 PMCID: PMC5805324 DOI: 10.1371/journal.pone.0192488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 01/24/2018] [Indexed: 12/14/2022] Open
Abstract
Dipeptidyl peptidase III (DPP III) isolated from the thermophilic bacteria Caldithrix abyssi (Ca) is a two-domain zinc exopeptidase, a member of the M49 family. Like other DPPs III, it cleaves dipeptides from the N-terminus of its substrates but differently from human, yeast and Bacteroides thetaiotaomicron (mesophile) orthologs, it has the pentapeptide zinc binding motif (HEISH) in the active site instead of the hexapeptide (HEXXGH). The aim of our study was to investigate structure, dynamics and activity of CaDPP III, as well as to find possible differences with already characterized DPPs III from mesophiles, especially B. thetaiotaomicron. The enzyme structure was determined by X-ray diffraction, while stability and flexibility were investigated using MD simulations. Using molecular modeling approach we determined the way of ligands binding into the enzyme active site and identified the possible reasons for the decreased substrate specificity compared to other DPPs III. The obtained results gave us possible explanation for higher stability, as well as higher temperature optimum of CaDPP III. The structural features explaining its altered substrate specificity are also given. The possible structural and catalytic significance of the HEISH motive, unique to CaDPP III, was studied computationally, comparing the results of long MD simulations of the wild type enzyme with those obtained for the HEISGH mutant. This study presents the first structural and biochemical characterization of DPP III from a thermophile.
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Affiliation(s)
- Igor Sabljić
- Division of Physical Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marko Tomin
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Mihaela Matovina
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Iva Sučec
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Tomašić Paić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Antonija Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Marija Abramić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sanja Tomić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Zagreb, Croatia
- * E-mail:
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13
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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).![]()
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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
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14
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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.
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15
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Kumar R, Maurya R, Saran S. Identification of novel inhibitors of the translationally controlled tumor protein (TCTP): insights from molecular dynamics. MOLECULAR BIOSYSTEMS 2017; 13:510-524. [PMID: 28128835 DOI: 10.1039/c6mb00850j] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The translationally controlled tumor protein (TCTP) is a highly conserved multifunctional protein, preferentially expressed in mitotically active tissues and is a potential biomarker and a therapeutic target for lung cancers. An understanding of the biology of this molecule and model systems for the screening of drugs is still awaited. In the absence of complete crystal structure, NMR structures as templates were used for homology modeling and MD optimization of both Dictyostelium discoideum and human TCTPs, which was followed by pocket-site prediction, ligand screening and docking. Rescoring of TCTP-ligand complexes was done using MD and MM-PBSA approaches. D. discoideum TCTP was expressed under a constitutive promoter and the endogenous RNA in multicellular structures formed was localized by in situ hybridization. Based on the interactions and binding energy scores, two novel compounds were identified as the best potential inhibitors that could be further used for the development of drug candidates. Inhibition of cell proliferation was observed in the strain overexpressing Dictyostelium TCTP and in situ hybridization results show them to be localized in the prestalk (dying cell population) cells. D. discoideum and human TCTPs share similar dynamic behaviors; overexpression of Dictyostelium TCTP inhibits cell proliferation. D. discoideum could be used as a model system for understanding the biology of this molecule and also for drug screening.
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Affiliation(s)
- Rakesh Kumar
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Ranjana Maurya
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
| | - Shweta Saran
- School of Life Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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16
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Matovina M, Agić D, Abramić M, Matić S, Karačić Z, Tomić S. New findings about human dipeptidyl peptidase III based on mutations found in cancer. RSC Adv 2017. [DOI: 10.1039/c7ra02642k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work we investigated the role of two highly conserved residues in the peptidase family M49, whose mutations G313W and R510W were detected in human cancer, using combined experimental and computational approaches.
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Affiliation(s)
- M. Matovina
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - D. Agić
- Josip Juraj Strossmayer University of Osijek
- Faculty of Agriculture in Osijek
- Osijek
- Croatia
| | - M. Abramić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - S. Matić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - Z. Karačić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
| | - S. Tomić
- Division of Organic Chemistry and Biochemistry
- Ruđer Bošković Institute
- Zagreb
- Croatia
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17
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Tomin M, Tomić S. Dynamic properties of dipeptidyl peptidase III from Bacteroides thetaiotaomicron and the structural basis for its substrate specificity – a computational study. MOLECULAR BIOSYSTEMS 2017; 13:2407-2417. [PMID: 28971197 DOI: 10.1039/c7mb00310b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Dynamics and enzyme activity of dipeptidyl peptidase III, wild type and mutants, from the human gut symbiont Bacteroides thetaiotaomicron.
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Affiliation(s)
- M. Tomin
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
| | - S. Tomić
- Division of Organic Chemistry and Biochemistry
- Rudjer Boskovic Institute
- Croatia
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18
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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.
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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
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