ArticleThe FEBS journal2018
Architecture and hydration of the arginine-binding site of neuropilin-1.
Article in The FEBS journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Machine learning-assisted identification and validation of NRP1 inhibitors through molecular docking and dynamics simulations.Scientific reports · 2026Article
- Structural and Energetic Insights into the Binding ofCell biochemistry and biophysics · 2025Article
- Neuropilin-1 as a Neuroinflammatory Entry Factor for SARS-CoV-2 Is Attenuated in Vaccinated COVID-19 Patients: A Case-Control Study.Health science reports · 2025Article
- Peptidomimetic inhibitors of the VEGF-AAmino acids · 2024Article
- New Crystal Form of Human Neuropilin-1 b1 Fragment with Six Electrostatic Mutations Complexed with KDKPPR Peptide Ligand.Molecules (Basel, Switzerland) · 2023Article
- Molecular dynamics simulations, docking and MMGBSA studies of newly designed peptide-conjugated glucosyloxy stilbene derivatives with tumor cell receptors.Molecular diversity · 2022Article
- Neuropilin (NRPs) Related Pathological Conditions and Their Modulators.International journal of molecular sciences · 2022Review
- VEGFA, B, C: Implications of the C-Terminal Sequence Variations for the Interaction with Neuropilins.Biomolecules · 2022Article
- Peptides Derived from Vascular Endothelial Growth Factor B Show Potent Binding to Neuropilin-1.Chembiochem : a European journal of chemical biology · 2022Article
- Article
- Tomato Bushy Stunt Virus Nanoparticles as a Platform for Drug Delivery to Shh-Dependent Medulloblastoma.International journal of molecular sciences · 2021Article
- Novel Compounds Targeting Neuropilin Receptor 1 with Potential To Interfere with SARS-CoV-2 Virus Entry.ACS chemical neuroscience · 2021Article
- The Role of VEGF Receptors as Molecular Target in Nuclear Medicine for Cancer Diagnosis and Combination Therapy.Cancers · 2021Review
- In silico drug repositioning against human NRP1 to block SARS-CoV-2 host entry.Turkish journal of biology = Turk biyoloji dergisi · 2021Article
- The role of Neuropilin-1 in COVID-19.PLoS pathogens · 2021Review
- In silico identification and validation of inhibitors of the interaction between neuropilin receptor 1 and SARS-CoV-2 Spike protein.bioRxiv : the preprint server for biology · 2020Article
- Biophysical screening methods for extracellular domain peptide receptors, application to natriuretic peptide receptor C ligands.Chemical biology & drug design · 2019Article
- Triazolopeptides Inhibiting the Interaction between Neuropilin-1 and Vascular Endothelial Growth Factor-165.Molecules (Basel, Switzerland) · 2019Article
- Neuropilins in the Context of Tumor Vasculature.International journal of molecular sciences · 2019Review
- Molecular Pharmacology of VEGF-A Isoforms: Binding and Signalling at VEGFR2.International journal of molecular sciences · 2018Review
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
Abstract
Neuropilin-1 (NRP1) is a transmembrane co-receptor involved in binding interactions with variety of ligands and receptors, including receptor tyrosine kinases. Expression of NRP1 in several cancers correlates with cancer stages and poor prognosis. Thus, NRP1 has been considered a therapeutic target and is the focus of multiple drug discovery initiatives. Vascular endothelial growth factor (VEGF) binds to the b1 domain of NRP1 through interactions between the C-terminal arginine of VEGF and residues in the NRP1-binding site including Tyr297, Tyr353, Asp320, Ser346 and Thr349. We obtained several complexes of the synthetic ligands and the NRP1-b1 domain and used X-ray crystallography and computational methods to analyse atomic details and hydration profile of this binding site. We observed side chain flexibility for Tyr297 and Asp320 in the six new high-resolution crystal structures of arginine analogues bound to NRP1. In addition, we identified conserved water molecules in binding site regions which can be targeted for drug design. The computational prediction of the VEGF ligand-binding site hydration map of NRP1 was in agreement with the experimentally derived, conserved hydration structure. Displacement of certain conserved water molecules by a ligand's functional groups may contribute to binding affinity, whilst other water molecules perform as protein-ligand bridges. Our report provides a comprehensive description of the binding site for the peptidic ligands' C-terminal arginines in the b1 domain of NRP1, highlights the importance of conserved structural waters in drug design and validates the utility of the computational hydration map prediction method in the context of neuropilin. DATABASE: The structures were deposited to the PDB with accession numbers PDB ID: 5IJR, 5IYY, 5JHK, 5J1X, 5JGQ, 5JGI.
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