1
|
Baiula M, Anselmi M, Musiani F, Ghidini A, Carbone J, Caligiana A, Maurizio A, Spampinato S, Gentilucci L. Design, Pharmacological Characterization, and Molecular Docking of Minimalist Peptidomimetic Antagonists of α 4β 1 Integrin. Int J Mol Sci 2023; 24:ijms24119588. [PMID: 37298541 DOI: 10.3390/ijms24119588] [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: 04/13/2023] [Revised: 05/17/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Integrin receptors mediate cell-cell interactions via the recognition of cell-adhesion glycoproteins, as well as via the interactions of cells with proteins of the extracellular matrix, and upon activation they transduce signals bi-directionally across the cell membrane. In the case of injury, infection, or inflammation, integrins of β2 and α4 families participate in the recruitment of leukocytes, a multi-step process initiated by the capturing of rolling leukocytes and terminated by their extravasation. In particular, α4β1 integrin is deeply involved in leukocyte firm adhesion preceding extravasation. Besides its well-known role in inflammatory diseases, α4β1 integrin is also involved in cancer, being expressed in various tumors and showing an important role in cancer formation and spreading. Hence, targeting this integrin represents an opportunity for the treatment of inflammatory disorders, some autoimmune diseases, and cancer. In this context, taking inspiration from the recognition motives of α4β1 integrin with its natural ligands FN and VCAM-1, we designed minimalist α/β hybrid peptide ligands, with our approach being associated with a retro strategy. These modifications are expected to improve the compounds' stability and bioavailability. As it turned out, some of the ligands were found to be antagonists, being able to inhibit the adhesion of integrin-expressing cells to plates coated with the natural ligands without inducing any conformational switch and any activation of intracellular signaling pathways. An original model structure of the receptor was generated using protein-protein docking to evaluate the bioactive conformations of the antagonists via molecular docking. Since the experimental structure of α4β1 integrin is still unknown, the simulations might also shed light on the interactions between the receptor and its native protein ligands.
Collapse
Affiliation(s)
- Monica Baiula
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Michele Anselmi
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale Fanin 40, 40126 Bologna, Italy
| | - Alessia Ghidini
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Jacopo Carbone
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Alberto Caligiana
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA
| | - Andrea Maurizio
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Santi Spampinato
- Department of Pharmacy and Biotechnology, University of Bologna, Via Irnerio 48, 40126 Bologna, Italy
| | - Luca Gentilucci
- Department of Chemistry "G. Ciamician", University of Bologna, Via Selmi 2, 40126 Bologna, Italy
- Health Sciences & Technologies (HST) CIRI, University of Bologna, 40064 Ozzano Emilia, Italy
| |
Collapse
|
2
|
Fakhoury JN, Zhang Y, Edmonds KA, Bringas M, Luebke JL, Gonzalez-Gutierrez G, Capdevila DA, Giedroc DP. Functional asymmetry and chemical reactivity of CsoR family persulfide sensors. Nucleic Acids Res 2021; 49:12556-12576. [PMID: 34755876 PMCID: PMC8643695 DOI: 10.1093/nar/gkab1040] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 01/14/2023] Open
Abstract
CstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
Collapse
Affiliation(s)
- Joseph N Fakhoury
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Yifan Zhang
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Katherine A Edmonds
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Mauro Bringas
- Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - Justin L Luebke
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA
| | - Giovanni Gonzalez-Gutierrez
- Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| | - Daiana A Capdevila
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Fundación Instituto Leloir, Av. Patricias Argentinas 435, Buenos Aires C1405BWE, Argentina
| | - David P Giedroc
- Department of Chemistry, Indiana University, 800 E. Kirkwood Ave, Bloomington, IN 47405-7102, USA.,Department of Molecular and Cellular Biochemistry, Indiana University, 212 S. Hawthorne Drive, Bloomington, IN 47405 USA
| |
Collapse
|
3
|
Musiani F, Broll V, Evangelisti E, Ciurli S. The model structure of the copper-dependent ammonia monooxygenase. J Biol Inorg Chem 2020; 25:995-1007. [PMID: 32926231 PMCID: PMC7584546 DOI: 10.1007/s00775-020-01820-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 09/02/2020] [Indexed: 12/24/2022]
Abstract
Abstract Ammonia monooxygenase is a copper-dependent membrane-bound enzyme that catalyzes the first step of nitrification in ammonia-oxidizing bacteria to convert ammonia to hydroxylamine, through the reductive insertion of a dioxygen-derived O atom in an N–H bond. This reaction is analogous to that carried out by particulate methane monooxygenase, which catalyzes the conversion of methane to methanol. The enzymatic activity of ammonia monooxygenase must be modulated to reduce the release of nitrogen-based soil nutrients for crop production into the atmosphere or underground waters, a phenomenon known to significantly decrease the efficiency of primary production as well as increase air and water pollution. The structure of ammonia monooxygenase is not available, rendering the rational design of enzyme inhibitors impossible. This study describes a successful attempt to build a structural model of ammonia monooxygenase, and its accessory proteins AmoD and AmoE, from Nitrosomonas europaea, taking advantage of the high sequence similarity with particulate methane monooxygenase and the homologous PmoD protein, for which crystal structures are instead available. The results obtained not only provide the structural details of the proteins ternary and quaternary structures, but also suggest a location for the copper-containing active site for both ammonia and methane monooxygenases, as well as support a proposed structure of a CuA-analogue dinuclear copper site in AmoD and PmoD. Graphic abstract ![]()
Electronic supplementary material The online version of this article (10.1007/s00775-020-01820-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Francesco Musiani
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| | - Valquiria Broll
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Elisa Evangelisti
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy
| | - Stefano Ciurli
- Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, 40127, Bologna, Italy.
| |
Collapse
|
4
|
Alfano M, Veronesi G, Musiani F, Zambelli B, Signor L, Proux O, Rovezzi M, Ciurli S, Cavazza C. A Solvent‐Exposed Cysteine Forms a Peculiar Ni
II
‐Binding Site in the Metallochaperone CooT from
Rhodospirillum rubrum. Chemistry 2019; 25:15351-15360. [DOI: 10.1002/chem.201903492] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Marila Alfano
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Giulia Veronesi
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Francesco Musiani
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Barbara Zambelli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Luca Signor
- IRIG, IBSUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| | - Olivier Proux
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Mauro Rovezzi
- OSUG, FAMEUniversity of Grenoble Alpes, CNRS, IRDIrstea, Météo France 38000 Grenoble France
| | - Stefano Ciurli
- Laboratory of Bioinorganic ChemistryDepartment of Pharmacy and BiotechnologyUniversity of Bologna Via Giuseppe Fanin 40 40127 Bologna Italy
| | - Christine Cavazza
- IRIG, CBMUniversity of Grenoble Alpes, CEA, CNRS 38000 Grenoble France
| |
Collapse
|
5
|
Abstract
Following the discovery of the first specific and essential role of nickel in biology in 1975 (the dinuclear active site of the enzyme urease) [...]
Collapse
|