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Goudiaby I, Malliavin TE, Mocchetti E, Mathiot S, Acherar S, Frochot C, Barberi-Heyob M, Guillot B, Favier F, Didierjean C, Jelsch C. New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand. Molecules 2023; 28:5603. [PMID: 37513474 PMCID: PMC10385628 DOI: 10.3390/molecules28145603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Neuropilin 1 (NRP1), a cell-surface co-receptor of a number of growth factors and other signaling molecules, has long been the focus of attention due to its association with the development and the progression of several types of cancer. For example, the KDKPPR peptide has recently been combined with a photosensitizer and a contrast agent to bind NRP1 for the detection and treatment by photodynamic therapy of glioblastoma, an aggressive brain cancer. The main therapeutic target is a pocket of the fragment b1 of NRP1 (NRP1-b1), in which vascular endothelial growth factors (VEGFs) bind. In the crystal packing of native human NRP1-b1, the VEGF-binding site is obstructed by a crystallographic symmetry neighbor protein, which prevents the binding of ligands. Six charged amino acids located at the protein surface were mutated to allow the protein to form a new crystal packing. The structure of the mutated fragment b1 complexed with the KDKPPR peptide was determined by X-ray crystallography. The variant crystallized in a new crystal form with the VEGF-binding cleft exposed to the solvent and, as expected, filled by the C-terminal moiety of the peptide. The atomic interactions were analyzed using new approaches based on a multipolar electron density model. Among other things, these methods indicated the role played by Asp320 and Glu348 in the electrostatic steering of the ligand in its binding site. Molecular dynamics simulations were carried out to further analyze the peptide binding and motion of the wild-type and mutant proteins. The simulations revealed that specific loops interacting with the peptide exhibited mobility in both the unbound and bound forms.
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Affiliation(s)
- Ibrahima Goudiaby
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
- Université Assane Seck de Ziguinchor, Laboratoire de Chimie et de Physique des Matériaux (LCPM), 523 Ziguinchor, Senegal
| | | | - Eva Mocchetti
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Sandrine Mathiot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Samir Acherar
- Université de Lorraine, CNRS, LCPM, F-54000 Nancy, France
| | - Céline Frochot
- Université de Lorraine, CNRS, LRGP, F-54000 Nancy, France
| | | | - Benoît Guillot
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Frédérique Favier
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Claude Didierjean
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
| | - Christian Jelsch
- Université de Lorraine, CNRS, CRM2, F-54000 Nancy, France; (I.G.); (E.M.); (B.G.)
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