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Turalić A, Đeđibegović J, Hegedüs Z, Martinek TA. DPP-4 Cleaves α/β-Peptide Bonds: Substrate Specificity and Half-Lives. Chembiochem 2020; 21:2060-2066. [PMID: 32180303 DOI: 10.1002/cbic.202000050] [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: 01/29/2020] [Revised: 02/19/2020] [Indexed: 11/07/2022]
Abstract
The incorporation of β-amino acids into a peptide sequence has gained particular attention as β- and α/β-peptides have shown remarkable proteolytic stability, even after a single homologation at the scissile bond. Several peptidases have been shown to cleave such bonds with high specificity but at a much slower rate compared to α-peptide bonds. In this study, a series of analogs of dipeptidyl peptidase-4 (DPP-4) substrate inhibitors were synthesized in order to investigate whether β-amino acid homologation at the scissile bond could be a valid approach to improving peptide stability towards DPP-4 degradation. DPP-4 cleaved the α/β-peptide bond after the N-terminal penultimate Pro with a broad specificity and retained full activity regardless of the β3 -amino acid side chain and peptide length. Significantly improved half-lives were observed for β3 Ile-containing peptides. Replacing the penultimate Pro with a conformationally constrained Pro mimetic led to proteolytic resistance. DPP-4 cleavage of α/β-peptide bonds with a broad promiscuity represents a new insight into the stability of peptide analogs containing β-amino acids as such analogs were thought to be stable towards enzymatic degradation.
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Affiliation(s)
- Amila Turalić
- Department of Pharmaceutical Analysis, University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Jasmina Đeđibegović
- Department of Pharmaceutical Analysis, University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged, Faculty of Medicine, 8 Dóm tér, 6720, Szeged, Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged, Faculty of Medicine, 8 Dóm tér, 6720, Szeged, Hungary.,MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, Szeged, 6720, Hungary
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2
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Masuda Y, Yoshida T, Yamaotsu N, Hirono S. Linear Discriminant Analysis for the <i>in Silico</i> Discovery of Mechanism-Based Reversible Covalent Inhibitors of a Serine Protease: Application of Hydration Thermodynamics Analysis and Semi-empirical Molecular Orbital Calculation. Chem Pharm Bull (Tokyo) 2018; 66:399-409. [DOI: 10.1248/cpb.c17-00854] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Yosuke Masuda
- School of Pharmaceutical Sciences, Kitasato University
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Engel M, Hoffmann T, Manhart S, Heiser U, Chambre S, Huber R, Demuth HU, Bode W. Rigidity and Flexibility of Dipeptidyl Peptidase IV: Crystal Structures of and Docking Experiments with DPIV. J Mol Biol 2006; 355:768-83. [PMID: 16330047 DOI: 10.1016/j.jmb.2005.11.014] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Revised: 11/02/2005] [Accepted: 11/04/2005] [Indexed: 11/18/2022]
Abstract
Dipeptidyl peptidase IV (DPIV) is an alpha,beta-hydrolase-like serine exopeptidase, which removes dipeptides, preferentially with a C-terminal l-Pro residue, from the N terminus of longer peptide substrates. Previously, we determined the tetrameric 1.8A crystal structure of native porcine DPIV. Each monomer is composed of a beta-propeller and a catalytic domain, which together embrace an internal cavity housing the active centre. This cavity is connected to the bulk solvent by a "propeller opening" and a "side opening". Here, we analyse DPIV complexes with a t-butyl-Gly-Pro-Ile tripeptide, Pro-boroPro, a piperazine purine compound, and aminoethyl phenyl sulfonylfluoride. The latter two compounds bind to the active-site groove in a compact and a quite bulky manner, respectively, causing considerable shifts of the catalytic Ser630 side-chain and of the Tyr547 phenolic group, which forms the oxyanion hole. The tripeptide, mimicking a peptide substrate, is clamped to the active site through tight interactions via its N-terminal alpha-ammonium group, the P2 carbonyl group, the P1-l-Pro side-chain, the C-terminal carboxylate group, and the stable orthoacid ester amide formed between the scissile peptide carbonyl group and Ser630 O(gamma). This stable trapping of the tripeptide could be due to stabilization of the protonated His740 imidazolium cation by the adjacent negatively charged C-terminal carboxylate group, preventing proton transfer to the leaving group nitrogen atom. Docking experiments with the compact rigid 58 residue protein aprotinin, which had been shown to be processed by DPIV, indicate that the Arg1-Pro2 N terminus can access the DPIV active site only upon widening of its side openings, probably by separation of the first and the last propeller blades, and/or of the catalytic and the propeller domain.
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Affiliation(s)
- Michael Engel
- Max-Planck-Institut für Biochemie, AG Proteinaseforschung, Am Klopferspitz 18, D-82152 Martinsried, Germany
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4
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Thoma R, Löffler B, Stihle M, Huber W, Ruf A, Hennig M. Structural basis of proline-specific exopeptidase activity as observed in human dipeptidyl peptidase-IV. Structure 2003; 11:947-59. [PMID: 12906826 DOI: 10.1016/s0969-2126(03)00160-6] [Citation(s) in RCA: 166] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Inhibition of dipeptidyl peptidase IV (DPP-IV), the main glucagon-like peptide 1 (GLP1)-degrading enzyme, has been proposed for the treatment of type II diabetes. We expressed and purified the ectodomain of human DPP-IV in Pichia pastoris and determined the X-ray structure at 2.1 A resolution. The enzyme consists of two domains, the catalytic domain, with an alpha/beta hydrolase fold, and a beta propeller domain with an 8-fold repeat of a four-strand beta sheet motif. The beta propeller domain contributes two important functions to the molecule that have not been reported for such structures, an extra beta sheet motif that forms part of the dimerization interface and an additional short helix with a double Glu sequence motif. The Glu motif provides recognition and a binding site for the N terminus of the substrates, as revealed by the complex structure with diprotin A, a substrate with low turnover that is trapped in the tetrahedral intermediate of the reaction in the crystal.
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Affiliation(s)
- Ralf Thoma
- F. Hoffmann-La Roche AG, Pharma Research Discovery, 4070 Basel, Switzerland
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Lambeir AM, Durinx C, Scharpé S, De Meester I. Dipeptidyl-peptidase IV from bench to bedside: an update on structural properties, functions, and clinical aspects of the enzyme DPP IV. Crit Rev Clin Lab Sci 2003; 40:209-94. [PMID: 12892317 DOI: 10.1080/713609354] [Citation(s) in RCA: 699] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Dipeptidyl-peptidase IV/CD26 (DPP IV) is a cell-surface protease belonging to the prolyloligopeptidase family. It selectively removes the N-terminal dipeptide from peptides with proline or alanine in the second position. Apart from its catalytic activity, it interacts with several proteins, for instance, adenosine deaminase, the HIV gp120 protein, fibronectin, collagen, the chemokine receptor CXCR4, and the tyrosine phosphatase CD45. DPP IV is expressed on a specific set of T lymphocytes, where it is up-regulated after activation. It is also expressed in a variety of tissues, primarily on endothelial and epithelial cells. A soluble form is present in plasma and other body fluids. DPP IV has been proposed as a diagnostic or prognostic marker for various tumors, hematological malignancies, immunological, inflammatory, psychoneuroendocrine disorders, and viral infections. DPP IV truncates many bioactive peptides of medical importance. It plays a role in glucose homeostasis through proteolytic inactivation of the incretins. DPP IV inhibitors improve glucose tolerance and pancreatic islet cell function in animal models of type 2 diabetes and in diabetic patients. The role of DPP IV/ CD26 within the immune system is a combination of its exopeptidase activity and its interactions with different molecules. This enables DPP IV/CD26 to serve as a co-stimulatory molecule to influence T cell activity and to modulate chemotaxis. DPP IV is also implicated in HIV-1 entry, malignant transformation, and tumor invasion.
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Affiliation(s)
- Anne-Marie Lambeir
- Department of Pharmaceutical Sciences, Laboratory of Medical Biochemistry, University of Antwerp, Universiteitsplein 1, Wilrijk, Belgium.
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Lambeir AM, Durinx C, Scharpé S, De Meester I. Dipeptidyl-Peptidase IV from Bench to Bedside: An Update on Structural Properties, Functions, and Clinical Aspects of the Enzyme DPP IV. Crit Rev Clin Lab Sci 2003. [DOI: 10.1080/713609354/?{alert(1)}] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/30/2022]
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Chapter 19. DPP-IV inhibition and therapeutic potential. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2001. [DOI: 10.1016/s0065-7743(01)36059-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Abstract
Quantum mechanical ab initio (RHF/6-31+G*//RHF/3-21G) calculations were used to simulate the formation of the tetrahedral complex intermediate (TC) in serine protease active site by substrates and transition-state analog inhibitors. The enzyme active site was simulated by an assembly of the amino acids participating in catalysis, whereas the substrates and inhibitors were simulated by small ligands, acetamide (1) and trifluoroacetone (2), respectively. For the first time, the principal factors determining the relative stability of the TC in serine proteases are arranged according to their energy contributions. These include (a) formation of the new covalent bond between Ser195 O(gamma) and the electrophilic center of a ligand; (b) stabilization of the oxyanion in the oxyanion hole; (c) basic catalysis by His57; and (d) hydrogen bond between Asp102 carboxylate and N(delta) of the protonated His57. We have directly calculated the gas-phase relative free energy of formation of TC(AS)(2) and TC(AS)(1), the value of DeltaDeltaG(g)[TC(AS)(2,1)]. It is DeltaE(cov), the relative energy of the new covalent bond between the enzyme and the ligand formed in a TC that determines the experimentally observed large difference in the stability of TCs formed by substrates and TS-analog inhibitors of serine proteases. We demonstrated that the relative stability of TCs formed by a series of mono- and dipeptide amides and TFKs, derived from experimental kinetic data, can be rather well approximated by the sum of the theoretically calculated value of DeltaDeltaG(g)[TC(AS)(2, 1)] and the difference in hydration free energies of isolated ligands.
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Affiliation(s)
- M Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
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Li GS, Maigret B, Rinaldi D, Ruiz-L�pez MF. Influence of environment on proton-transfer mechanisms in model triads from theoretical calculations. J Comput Chem 1998. [DOI: 10.1002/(sici)1096-987x(19981130)19:15<1675::aid-jcc1>3.0.co;2-k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Nguyen C, Blanco J, Mazaleyrat JP, Krust B, Callebaut C, Jacotot E, Hovanessian AG, Wakselman M. Specific and irreversible cyclopeptide inhibitors of dipeptidyl peptidase IV activity of the T-cell activation antigen CD26. J Med Chem 1998; 41:2100-10. [PMID: 9622551 DOI: 10.1021/jm970640l] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The dipeptidyl peptidase IV (DPP IV) activity of CD26 is characterized by its post-proline-cleaving capacity that plays an important but not yet understood role in biological processes. Here we describe a new family of specific and irreversible inhibitors of this enzyme. Taking into account the substrate specificity of DPP IV for P2-P1><-P1' cleavage, we have designed and synthesized cyclopeptides c[(alphaH2N+)-Lys-Pro-Aba-(6-CH2-S+R2)-Glyn] 2TFA- (Aba = 3-aminobenzoic acid, R = alkyl) possessing a proline at the P1 position and a lysine in the P2 position, which allows the closing of the cycle on its side chain. These molecules show a free N-terminus, necessary for binding to the CD26 catalytic site, and a latent quinoniminium methide electrophile, responsible for inactivation. Treatment of c[alphaZ-Lys-Pro-Aba-(6-CH2-OC6H5)-Glyn], obtained by peptide synthesis in solution, with R2S/TFA simutaneously cleaved the Z protecting group and the phenyl ether function and led to a series of cyclopeptide sulfonium salts. These cyclopeptides inhibited rapidly and irreversibly the DPP IV activity of CD26, with IC50 values in the nanomolar range. Further studies were carried out to investigate the effect of the modification of the ring size (n = 2 or 4) and the nature of the sulfur substituents (R = Me, Bu, Oct). Cycle enlargement improved the inhibitory activity of the methylsulfonio cyclopeptide, whereas the increase of the alkyl chain length on the sulfur atom had no apparent effect. Other aminopeptidases were not inhibited, and a much weaker activity was observed on a novel isoform of DPP IV referred to as DPP IV-beta. Thus, this new family of irreversible inhibitors of DPP IV is highly specific to the peptidase activity of CD26.
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Affiliation(s)
- C Nguyen
- SIRCOB, Université de Versailles, Bâtiment Lavoisier, 45 avenue des Etats Unis, F-78000 Versailles, France
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11
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Abstract
Proline is unique among the 20 amino acids due to its cyclic structure. This specific conformation imposes many restrictions on the structural aspects of peptides and proteins and confers particular biological properties upon a wide range of physiologically important biomolecules. In order to adequately deal with such peptides, nature has developed a group of enzymes that recognise this residue specifically. These peptidases cover practically all situations where a proline residue might occur in a potential substrate. In this paper we endeavour to discuss these enzymes, particularly those responsible for peptide or protein hydrolysis at proline sites. We have detailed their discovery, biochemical attributes and substrate specificities and have provided information as to the methodology used to detect and manipulate their activities. We have also described the roles, or potential roles that these enzymes may play physiologically and the consequences of their dysfunction in varied disease states.
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Affiliation(s)
- D F Cunningham
- School of Biological Sciences, Dublin City University, Dublin, Ireland
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12
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Brandt W. A molecular model of the active site of dipeptidyl peptidase IV. Explanation of the substrate specificity and interaction with inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 1997; 421:171-8. [PMID: 9330694 DOI: 10.1007/978-1-4757-9613-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- W Brandt
- Martin-Luther-Universität Halle-Wittenberg, Germany
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