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Tymecka D, Redkiewicz P, Lipiński PFJ, Misicka A. Peptidomimetic inhibitors of the VEGF-A 165/NRP-1 complex obtained by modification of the C-terminal arginine. Amino Acids 2024; 56:49. [PMID: 39181965 PMCID: PMC11344719 DOI: 10.1007/s00726-024-03411-8] [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: 06/28/2024] [Accepted: 08/18/2024] [Indexed: 08/27/2024]
Abstract
Inhibitors of the interaction between Neuropilin-1 (NRP-1) and Vascular Endothelial Growth Factor-A165 (VEGF-A165) hold significant promise as therapeutic and diagnostic agents directed against cancers overexpressing NRP-1. In our efforts in this field, a few series of strong and fairly stable peptide-like inhibitors of the general formula Lys(Har)1-Xaa2-Xaa3-Arg4 have been previously discovered. In the current work, we focused on Lys(Har)-Dap/Dab-Pro-Arg sequence. The aim was to examine whether replacing C-terminal Arg with its homologs and mimetics would yield more stable yet still potent inhibitors. Upon considering the results of modelling and other factors, ten novel analogues with Xaa4 = homoarginine (Har), 2-amino-4-guanidino-butyric acid (Agb), 2-amino-3-guanidino-propionic acid (Agp), citrulline (Cit), 4-aminomethyl-phenylalanine [Phe(4-CH2-NH2)] were designed, synthesized and evaluated. Two of the proposed modifications resulted in inhibitors with activity slightly lower [e.g. IC50 = 14.3 μM for Lys(Har)-Dab-Pro-Har and IC50 = 19.8 μM for Lys(Har)-Dab-Pro-Phe(4-CH2-NH2)] than the parent compounds [e.g. IC50 = 4.7 μM for Lys(Har)-Dab-Pro-Arg]. What was a surprise to us, the proteolytic stability depended more on position two of the sequence than on position four. The Dab2-analogues exhibited half-life times beyond 60 h. Our results build up the knowledge on the structural requirements that effective VEGF-A165/NRP-1 inhibitors should fulfil.
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Affiliation(s)
- Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
| | - Patrycja Redkiewicz
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Institute Polish Academy of Sciences, Pawińskiego 5, 02-106, Warsaw, Poland
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093, Warsaw, Poland.
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2
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Fedorczyk B, Redkiewicz P, Matalińska J, Piast R, Kosson P, Wieczorek R. Chirality and Rigidity in Triazole-Modified Peptidomimetics Interacting with Neuropilin-1. Pharmaceuticals (Basel) 2024; 17:190. [PMID: 38399405 PMCID: PMC10891769 DOI: 10.3390/ph17020190] [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: 11/27/2023] [Revised: 01/19/2024] [Accepted: 01/19/2024] [Indexed: 02/25/2024] Open
Abstract
The interaction of Neuropilin-1 (NRP-1) with vascular endothelial growth factor (VEGF) has been shown to promote angiogenesis under physiological and pathological conditions. Angiogenesis around tumors is a major factor allowing for their growth and spread. Disrupting NRP-1/VEGF complex formation is thus a promising pathway for the development of new anticancer pharmaceuticals. A large body of work has been produced in the last two decades detailing the development of inhibitors of NRP-1/VEGF complex formation. Among those were peptide A7R and its smaller derivatives KXXR and K(Har)XXR. It has been previously reported that replacement of the XX backbone with triazole residues has a positive effect on the proteolytic stability of inhibitors. It has also been reported that a higher dihedral angle range restriction of the XX backbone has a positive effect on the activity of inhibitors. In this work, we have designed new triazole derivatives of K(Har)XXR inhibitors with substitution allowing for higher range restriction of the XX backbone. The obtained peptidomimetics have greater activity than their less restricted counterparts. One of the newly obtained structures has greater affinity than the reference peptide A7R.
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Affiliation(s)
- Bartłomiej Fedorczyk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (B.F.); (R.P.)
| | - Patrycja Redkiewicz
- Mossakowski Medical Research Centre Polish Academy of Science, 5 Pawinskiego Street, 02-106 Warsaw, Poland; (P.R.); (J.M.); (P.K.)
| | - Joanna Matalińska
- Mossakowski Medical Research Centre Polish Academy of Science, 5 Pawinskiego Street, 02-106 Warsaw, Poland; (P.R.); (J.M.); (P.K.)
| | - Radosław Piast
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (B.F.); (R.P.)
| | - Piotr Kosson
- Mossakowski Medical Research Centre Polish Academy of Science, 5 Pawinskiego Street, 02-106 Warsaw, Poland; (P.R.); (J.M.); (P.K.)
| | - Rafał Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (B.F.); (R.P.)
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3
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Puszko AK, Sosnowski P, Hermine O, Hopfgartner G, Lepelletier Y, Misicka A. Structure-activity relationship studies and biological properties evaluation of peptidic NRP-1 ligands: Investigation of N-terminal cysteine importance. Bioorg Med Chem 2023; 94:117482. [PMID: 37774449 DOI: 10.1016/j.bmc.2023.117482] [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: 06/20/2023] [Revised: 09/19/2023] [Accepted: 09/20/2023] [Indexed: 10/01/2023]
Abstract
Neuropilin-1 (NRP-1) is a major co-receptor of vascular endothelial growth factor receptor-2 (VEGFR-2). It may also stimulate tumour growth and metastasis independently of VEGF-A165. These functions make VEGF-A165/NRP-1 complex formation and its inhibition of great interest, where NRP-1 is the target for which effective ligands are sought. Design of peptide-like inhibitors represent a strategy with great potential in the treatment of NRP-1-related disorders. Here, we present the synthesis, molecular modelling, structure-activity relationship studies as well as biological evaluation of peptides with the branched sequences H2N-X-Lys(hArg)-Dab-Oic-Arg-OH and H2N-Lys(X-hArg)-Dab-Oic-Arg-OH. Two of the designed peptides, in which Cys was inserted in X position, expressed high affinity (∼40 nM value) for NRP-1 and were resistant to enzymatic digestion in human serum. Moreover, peptide/NRP-1 complex promoted fast intracytoplasmic protein trafficking towards the plasma membrane in breast cancer cells. Our results suggest that these compounds might be good candidates for further development of VEGF-A165/NRP-1 inhibitors.
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Affiliation(s)
- Anna K Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Piotr Sosnowski
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland; Department of Bioanalytics, Medical University of Lublin, Jaczewskiego 8b, 20-090 Lublin, Poland
| | - Olivier Hermine
- Université Paris Cité, Imagine Institute, 24 boulevard Montparnasse, 75015 Paris, France; INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
| | - Gérard Hopfgartner
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Yves Lepelletier
- Université Paris Cité, Imagine Institute, 24 boulevard Montparnasse, 75015 Paris, France; INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 boulevard Montparnasse, 75015 Paris, France
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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Sabki A, Khelifi L, Kameli A, Baali S. Identification of Four New Chemical Series of Small Drug-Like Natural Products as Potential Neuropilin-1 Inhibitors by Structure-Based Virtual Screening: Pharmacophore-Based Molecular Docking and Dynamics Simulation. Chem Biodivers 2023; 20:e202200933. [PMID: 36799050 DOI: 10.1002/cbdv.202200933] [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: 10/01/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/18/2023]
Abstract
Neuropilin-1 (NRP-1), a surface transmembrane glycoprotein, is one of the most important co-receptors of VEGF-A165 (vascular endothelial growth factor) responsible for pathological angiogenesis. In general, NRP-1 overexpression in cancer correlates with poor prognosis and more tumor aggressiveness. NRP-1 role in cancer has been mainly explained by mediating VEGF-A165-induced effects on tumor angiogenesis. NRP-1 was recently identified as a co-receptor and an independent gateway for SARS-CoV-2 through binding subunit S2 of Spike protein in the same way as VEGF-A165. Thus, NRP-1 is of particular value as a target for cancer therapy and other angiogenesis-dependent diseases as well as for SARS-CoV-2 antiviral intervention. Herein, The Super Natural II, the largest available database of natural products (∼0.33 M), pre-filtered with drug-likeness criteria (absorption, distribution, metabolism and excretion/toxicity), was screened against NRP-1. NRP-1/VEGF-A165 interaction is one of protein-protein interfaces (PPIs) known to be challenging when approached in-silico. Thus, a PPI-suited multi-step virtual screening protocol, incorporating a derived pharmacophore with molecular docking and followed by MD (molecular dynamics) simulation, was designed. Two stages of pharmacophorically constrained molecular docking (standard and extra precisions), a mixed Torsional/Low-mode conformational search and MM-GBSA ΔG binding affinities calculation, resulted in the selection of 100 hits. These 100 hits were subjected to 20 ns MD simulation, that was extended to 100 ns for top hits (20) and followed by post-dynamics analysis (atomic ligand-protein contacts, RMSD, RMSF, MM-GBSA ΔG, Rg, SASA and H-bonds). Post-MD analysis showed that 19 small drug-like nonpeptide natural molecules, grouped in four chemical scaffolds (purine, thiazole, tetrahydropyrimidine and dihydroxyphenyl), well verified the derived pharmacophore and formed stable and compact complexes with NRP-1. The discovered molecules are promising and can serve as a base for further development of new NRP-1 inhibitors.
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Affiliation(s)
- Abdellah Sabki
- Laboratory of Genetic Resources & Biotechnology, National School of Agricultural Sciences (ENSA), 16004, Algiers, Algeria
| | - Lakhdar Khelifi
- Laboratory of Genetic Resources & Biotechnology, National School of Agricultural Sciences (ENSA), 16004, Algiers, Algeria
| | - Abdelkrim Kameli
- Laboratory of Ethnobotany and Natural Substances, Department of Natural Sciences, ENS Kouba, 16050, Algiers, Algeria
| | - Salim Baali
- Laboratory of Ethnobotany and Natural Substances, Department of Natural Sciences, ENS Kouba, 16050, Algiers, Algeria
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Scandium-44 Radiolabeled Peptide and Peptidomimetic Conjugates Targeting Neuropilin-1 Co-Receptor as Potential Tools for Cancer Diagnosis and Anti-Angiogenic Therapy. Biomedicines 2023; 11:biomedicines11020564. [PMID: 36831099 PMCID: PMC9953004 DOI: 10.3390/biomedicines11020564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Pathological angiogenesis, resulting from an imbalance between anti- and pro-angiogenic factors, plays a pivotal role in tumor growth, development and metastasis. The inhibition of the angiogenesis process by the VEGF/VEGFR-2/NRP-1 pathway raises interest in the search for such interaction inhibitors for the purpose of the early diagnosis and treatment of angiogenesis-dependent diseases. In this work we designed and tested peptide-based radiocompounds that selectively bind to the neuropilin-1 co-receptor and prevent the formation of the pro-angiogenic VEGF-A165/NRP-1 complex. Three biomolecules, A7R and retro-inverso DR7A peptides, and the branched peptidomimetic Lys(hArg)-Dab-Pro-Arg (K4R), conjugated with macrocyclic chelator through two linkers' types, were labeled with theranostic scandium-44 radionuclide, and studied in vitro as potential targeted radiopharmaceuticals. ELISA (enzyme-linked immunosorbent assay) studies showed no negative effect of the introduced biomolecules' changes and high NRP-1 affinity in the case of A7R- and K4R-radiocompounds and a lack affinity for DR7A-radiocompounds. All radiopeptides showed a hydrophilic nature as well as high stability against ligand exchange reactions in cysteine/histidine solutions. Unfortunately, all radiocompounds showed unsatisfactory nano-scale stability in human serum, especially for use as therapeutic radioagents. Further work is ongoing and focused on the search for angiogenesis inhibitors that are more human serum stable.
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Karami E, Mesbahi Moghaddam M, Behdani M, Kazemi-Lomedasht F. Effective blocking of neuropilin-1activity using oligoclonal nanobodies targeting different epitopes. Prep Biochem Biotechnol 2022; 53:523-531. [PMID: 35984637 DOI: 10.1080/10826068.2022.2111583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Neuropilin-1 (NRP-1) is a non-tyrosine kinase receptor and when overexpressed, leads to angiogenesis. High expression of NRP-1 has been observed in various cancers. Unique characteristic of nanobodies (small size, high affinity and stability, and ease production) make them potential therapeutic tools. Oligoclonal nanobodies which detect multiple functional epitopes on the target antigen could be potential tools for inhibition of cancer resistance problems due to escape variant of tumor cells. In this study, oligoclonal anti-NRP-1 nanobodies were selected from camel immune library and their binding activities as well as in vitro functionality were evaluated. Anti-NRP-1 nanobodies were expressed in an Escherichia coli host, and purified using nickel affinity chromatography. The effect of each individual and oligoclonal nanobodies on human endothelial cells were evaluated by MTT, Tube formation, and migration assay as well. Results showed that oligoclonal anti-NRP-1 nanobodies detected different epitopes of NRP-1 antigen and inhibited in vitro angiogenesis of human endothelial cells better than each individual nanobody. Results indicate promising oligoclonal anti-NRP-1 nanobodies for inhibition of angiogenesis.
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Affiliation(s)
- Elmira Karami
- Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | | | - Mahdi Behdani
- Venom and Biotherapeuti Molcsecules Laboratory, Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Fatemeh Kazemi-Lomedasht
- Biotechnology Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
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7
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Novel Small-Molecule Inhibitors of the SARS-CoV-2 Spike Protein Binding to Neuropilin 1. Pharmaceuticals (Basel) 2022; 15:ph15020165. [PMID: 35215277 PMCID: PMC8879887 DOI: 10.3390/ph15020165] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 12/18/2021] [Accepted: 01/26/2022] [Indexed: 12/04/2022] Open
Abstract
Furin cleavage of the SARS-CoV-2 spike protein results in a polybasic terminal sequence termed the C-end rule (CendR), which is responsible for the binding to neuropilin 1 (NRP1), enhancing viral infectivity and entry into the cell. Here we report the identification of 20 small-molecule inhibitors that emerged from a virtual screening of nearly 950,000 drug-like compounds that bind with high probability to the CendR-binding pocket of NRP1. In a spike NRP1 binding assay, two of these compounds displayed a stronger inhibition of spike protein binding to NRP1 than the known NRP1 antagonist EG00229, for which the inhibition of the CendR peptide binding to NRP1 was also experimentally confirmed. These compounds present a good starting point for the design of small-molecule antagonists against the SARS-CoV-2 viral entry.
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8
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Masłowska K, Witkowska E, Tymecka D, Halik PK, Misicka A, Gniazdowska E. Synthesis, Physicochemical and Biological Study of Gallium-68- and Lutetium-177-Labeled VEGF-A 165/NRP-1 Complex Inhibitors Based on Peptide A7R and Branched Peptidomimetic. Pharmaceutics 2022; 14:pharmaceutics14010100. [PMID: 35056995 PMCID: PMC8779334 DOI: 10.3390/pharmaceutics14010100] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 02/01/2023] Open
Abstract
Neuropilin-1 (NRP-1) is a surface receptor found on many types of cancer cells. The overexpression of NRP-1 and its interaction with vascular endothelial growth factor-165 (VEGF165) are associated with tumor growth and metastasis. Therefore, compounds that block the VEGF165/NRP-1 interaction represent a promising strategy to image and treat NRP-1-related pathologies. The aim of the presented work was to design and synthesize radioconjugates of two known peptide-type inhibitors of the VEGF165/NRP-1 complex: A7R peptide and its shorter analog, the branched peptidomimetic Lys(hArg)-Dab-Pro-Arg. Both peptide-type inhibitors were coupled to a radionuclide chelator (DOTA) via a linker (Ahx) and so radiolabeled with Ga-68 and Lu-177 radionuclides, for diagnostic and therapeutic uses, respectively. The synthesized radioconjugates were tested for their possible use as theranostic-like radiopharmaceuticals for the imaging and therapy of cancers that overexpress NRP-1. The obtained results indicate good efficiency of the radiolabeling reaction and satisfactory stability, at least 3t1/2 for the 68Ga- and 1t1/2 for the 177Lu-radiocompounds, in solutions mimicking human body fluids. However, enzymatic degradation of both the studied inhibitors caused insufficient stability of the radiocompounds in human serum, indicating that further modifications are needed to sufficiently stabilize the peptidomimetics with inhibitory properties against VEGF165/NRP-1 complex formation.
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Affiliation(s)
- Katarzyna Masłowska
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
- Correspondence: (K.M.); (A.M.)
| | - Ewa Witkowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
| | - Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
| | - Paweł Krzysztof Halik
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland; (E.W.); (D.T.)
- Correspondence: (K.M.); (A.M.)
| | - Ewa Gniazdowska
- Centre of Radiochemistry and Nuclear Chemistry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195 Warsaw, Poland; (P.K.H.); (E.G.)
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Perez-Miller S, Patek M, Moutal A, de Haro PD, Cabel CR, Thorne CA, Campos SK, Khanna R. Novel Compounds Targeting Neuropilin Receptor 1 with Potential To Interfere with SARS-CoV-2 Virus Entry. ACS Chem Neurosci 2021; 12:1299-1312. [PMID: 33787218 PMCID: PMC8029449 DOI: 10.1021/acschemneuro.0c00619] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/22/2021] [Indexed: 12/15/2022] Open
Abstract
Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 Spike protein interferes with pain signaling. Here, we report confirmed hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physicochemical properties. Using ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Further, two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.
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Affiliation(s)
- Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona, USA
| | - Marcel Patek
- Bright Rock Path Consulting, LLC, Tucson, Arizona
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Paz Duran de Haro
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Carly R. Cabel
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
| | - Curtis A. Thorne
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
| | - Samuel K. Campos
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
- Department of Immunobiology, College of Medicine, University of Arizona
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona, USA
- Regulonix LLC, Tucson, AZ, USA
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Mone P, Gambardella J, Wang X, Jankauskas SS, Matarese A, Santulli G. miR-24 targets SARS-CoV-2 co-factor Neuropilin-1 in human brain microvascular endothelial cells: Insights for COVID-19 neurological manifestations. RESEARCH SQUARE 2021:rs.3.rs-192099. [PMID: 33564755 PMCID: PMC7872362 DOI: 10.21203/rs.3.rs-192099/v1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neuropilin-1 is a transmembrane glycoprotein that has been implicated in several processes including angiogenesis and immunity. Recent evidence has also shown that it is implied in the cellular internalization of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19). We hypothesized that specific microRNAs can target Neuropilin-1. By combining bioinformatic and functional approaches, we identified miR-24 as a regulator of Neuropilin-1 transcription. Since Neuropilin-1 has been shown to play a key role in the endothelium-mediated regulation of the blood-brain barrier, we validated miR-24 as a functional modulator of Neuropilin-1 in human brain microvascular endothelial cells (hBMECs), which are the most suitable cell line for an in vitro bloodâ€"brain barrier model.
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Mone P, Gambardella J, Wang X, Jankauskas SS, Matarese A, Santulli G. miR-24 Targets the Transmembrane Glycoprotein Neuropilin-1 in Human Brain Microvascular Endothelial Cells. Noncoding RNA 2021; 7:9. [PMID: 33540664 PMCID: PMC7931075 DOI: 10.3390/ncrna7010009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 02/06/2023] Open
Abstract
Neuropilin-1 is a transmembrane glycoprotein that has been implicated in several processes including angiogenesis and immunity. Recent evidence has also shown that it is implied in the cellular internalization of the severe acute respiratory syndrome coronavirus (SARS-CoV-2), which causes the coronavirus disease 2019 (COVID-19). We hypothesized that specific microRNAs can target Neuropilin-1. By combining bioinformatic and functional approaches, we identified miR-24 as a regulator of Neuropilin-1 transcription. Since Neuropilin-1 has been shown to play a key role in the endothelium-mediated regulation of the blood-brain barrier, we validated miR-24 as a functional modulator of Neuropilin-1 in human brain microvascular endothelial cells (hBMECs), which are the most suitable cell line for an in vitro blood-brain barrier model.
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Affiliation(s)
- Pasquale Mone
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Albert Einstein College of Medicine, New York, NY 10461, USA; (P.M.); (J.G.); (X.W.); (S.S.J.)
- Department of Advanced Medical and Surgical Sciences, University of Campania “Luigi Vanvitelli”, 80100 Naples, Italy
| | - Jessica Gambardella
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Albert Einstein College of Medicine, New York, NY 10461, USA; (P.M.); (J.G.); (X.W.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
- Department of Advanced Biomedical Science, “Federico II” University, and International Translational Research and Medical Education (ITME), 80131 Naples, Italy
| | - Xujun Wang
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Albert Einstein College of Medicine, New York, NY 10461, USA; (P.M.); (J.G.); (X.W.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
| | - Stanislovas S. Jankauskas
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Albert Einstein College of Medicine, New York, NY 10461, USA; (P.M.); (J.G.); (X.W.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
| | | | - Gaetano Santulli
- Department of Medicine, Division of Cardiology, Wilf Family Cardiovascular Research Institute, Einstein Institute for Aging Research, Albert Einstein College of Medicine, New York, NY 10461, USA; (P.M.); (J.G.); (X.W.); (S.S.J.)
- Department of Molecular Pharmacology, Einstein-Mount Sinai Diabetes Research Center (ES-DRC), Fleischer Institute for Diabetes and Metabolism (FIDAM), Albert Einstein College of Medicine, New York, NY 10461, USA
- Department of Advanced Biomedical Science, “Federico II” University, and International Translational Research and Medical Education (ITME), 80131 Naples, Italy
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Puszko AK, Sosnowski P, Rignault-Bricard R, Hermine O, Hopfgartner G, Pułka-Ziach K, Lepelletier Y, Misicka A. Urea-Peptide Hybrids as VEGF-A 165/NRP-1 Complex Inhibitors with Improved Receptor Affinity and Biological Properties. Int J Mol Sci 2020; 22:ijms22010072. [PMID: 33374715 PMCID: PMC7793531 DOI: 10.3390/ijms22010072] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 12/31/2022] Open
Abstract
Neuropilin-1 (NRP-1), the major co-receptor of vascular endothelial growth factor receptor-2 (VEGFR-2), may also independently act with VEGF-A165 to stimulate tumour growth and metastasis. Therefore, there is great interest in compounds that can block VEGF-A165/NRP-1 interaction. Peptidomimetic type inhibitors represent a promising strategy in the treatment of NRP-1-related disorders. Here, we present the synthesis, affinity, enzymatic stability, molecular modeling and in vitro binding evaluation of the branched urea–peptide hybrids, based on our previously reported Lys(hArg)-Dab-Oic-Arg active sequence, where the Lys(hArg) branching has been modified by introducing urea units to replace the peptide bond at various positions. One of the resulting hybrids increased the affinity of the compound for NRP-1 more than 10-fold, while simultaneously improving resistance for proteolytic stability in serum. In addition, ligand binding to NRP-1 induced rapid protein stock exocytotic trafficking to the plasma membrane in breast cancer cells. Examined properties characterize this compound as a good candidate for further development of VEGF165/NRP-1 inhibitors.
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Affiliation(s)
- Anna K. Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Correspondence: (A.K.P.); (A.M.)
| | - Piotr Sosnowski
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland; (P.S.); (G.H.)
| | - Rachel Rignault-Bricard
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (R.R.-B.); (O.H.); (Y.L.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 Boulevard Montparnasse, 75015 Paris, France
| | - Olivier Hermine
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (R.R.-B.); (O.H.); (Y.L.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 Boulevard Montparnasse, 75015 Paris, France
| | - Gérard Hopfgartner
- Department of Inorganic and Analytical Chemistry, University of Geneva, 24 Quai Ernest Ansermet, CH-1211 Geneva, Switzerland; (P.S.); (G.H.)
| | | | - Yves Lepelletier
- Imagine Institute, Université de Paris, 24 boulevard Montparnasse, 75015 Paris, France; (R.R.-B.); (O.H.); (Y.L.)
- INSERM UMR 1163, Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications, 24 Boulevard Montparnasse, 75015 Paris, France
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland;
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland
- Correspondence: (A.K.P.); (A.M.)
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13
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Perez-Miller S, Patek M, Moutal A, Cabel CR, Thorne CA, Campos SK, Khanna R. 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 2020:2020.09.22.308783. [PMID: 32995772 PMCID: PMC7523098 DOI: 10.1101/2020.09.22.308783] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Neuropilin-1 (NRP-1) is a multifunctional transmembrane receptor for ligands that affect developmental axonal growth and angiogenesis. In addition to a role in cancer, NRP-1 is a reported entry point for several viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causal agent of coronavirus disease 2019 (COVID-19). The furin cleavage product of SARS-CoV-2 Spike protein takes advantage of the vascular endothelial growth factor A (VEGF-A) binding site on NRP-1 which accommodates a polybasic stretch ending in a C-terminal arginine. This site has long been a focus of drug discovery efforts for cancer therapeutics. We recently showed that interruption of the VEGF-A/NRP-1 signaling pathway ameliorates neuropathic pain and hypothesize that interference of this pathway by SARS-CoV-2 spike protein interferes with pain signaling. Here, we report hits from a small molecule and natural product screen of nearly 0.5 million compounds targeting the VEGF-A binding site on NRP-1. We identified nine chemical series with lead- or drug-like physico-chemical properties. Using an ELISA, we demonstrate that six compounds disrupt VEGF-A-NRP-1 binding more effectively than EG00229, a known NRP-1 inhibitor. Secondary validation in cells revealed that almost all tested compounds inhibited VEGF-A triggered VEGFR2 phosphorylation. Two compounds displayed robust inhibition of a recombinant vesicular stomatitis virus protein that utilizes the SARS-CoV-2 Spike for entry and fusion. These compounds represent a first step in a renewed effort to develop small molecule inhibitors of the VEGF-A/NRP-1 signaling for the treatment of neuropathic pain and cancer with the added potential of inhibiting SARS-CoV-2 virus entry.
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Affiliation(s)
- Samantha Perez-Miller
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona 85724, USA
| | - Marcel Patek
- Bright Rock Path Consulting, LLC, Tucson, Arizona
| | - Aubin Moutal
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Carly R. Cabel
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
| | - Curtis A. Thorne
- Department of Cellular & Molecular Medicine, College of Medicine, The University of Arizona
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
| | - Samuel K. Campos
- Cancer Biology Graduate Interdisciplinary Program, University of Arizona
- Bio5 Institute, University of Arizona
- Department of Immunobiology, College of Medicine, University of Arizona
| | - Rajesh Khanna
- Department of Pharmacology, College of Medicine, The University of Arizona, Tucson, AZ, United States
- The Center for Innovation in Brain Sciences, The University of Arizona Health Sciences, Tucson, Arizona 85724, USA
- Regulonix LLC, 1555 E. Entrada Segunda, Tucson, AZ 85718, USA
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14
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Chen C, Zhang R, Ma L, Li Q, Zhao YL, Zhang GJ, Zhang D, Li WZ, Cao S, Wang L, Geng ZM. Neuropilin-1 is up-regulated by cancer-associated fibroblast-secreted IL-8 and associated with cell proliferation of gallbladder cancer. J Cell Mol Med 2020; 24:12608-12618. [PMID: 32951327 PMCID: PMC7686964 DOI: 10.1111/jcmm.15825] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/22/2020] [Accepted: 08/13/2020] [Indexed: 01/04/2023] Open
Abstract
We previously demonstrated that cancer‐associated fibroblasts (CAFs) promoted the proliferation of gallbladder cancer (GBC) cells, but the mechanism is not clear. Neuropilin‐1 (NRP‐1) plays an important role in various malignancies as transmembrane glycoprotein. Our goal was to reveal the relationship between CAFs and NRP‐1 and their potential functions in GBC. In this study, we found NRP‐1 was overexpressed in GBC tissue, associated with poor survival and was up‐regulated by CAFs. The cytokine array cluster analysis revealed IL‐8 secreted by CAFs facilitated the up‐regulation of NRP‐1 in tumour cells. NRP‐1 knockdown suppressed tumour growth in vivo. Gene expression microarray analysis showed 581 differentially regulated genes under NRP‐1 knockdown conditions. Ingenuity pathway analysis demonstrated that NRP‐1 knockdown may inhibit tumour progression by affecting cell proliferation. We then confirmed that NRP‐1 knockdown in NOZ and GBC‐SD cells significantly inhibited cell proliferation. Additionally, the IL‐8 mediated MDM2 and CCNA2 expression were affected by NRP‐1 knockdown. Our findings suggested that NRP‐1 was up‐regulated by CAF‐secreted IL‐8, which subsequently promoted GBC cell proliferation, and these molecules may serve as useful prognostic biomarkers and therapeutic targets for GBC.
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Affiliation(s)
- Chen Chen
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Rui Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Li Ma
- Department of Emergency, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Qi Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Ya-Ling Zhao
- Department of of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University, Health Science Center, Xi'an, Shaanxi Province, China
| | - Guan-Jun Zhang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Dong Zhang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Wen-Zhi Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Sheng Cao
- Gastroenterology Research Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lin Wang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Zhi-Min Geng
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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15
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Fedorczyk B, Lipiński PFJ, Puszko AK, Tymecka D, Wilenska B, Dudka W, Perret GY, Wieczorek R, Misicka A. Triazolopeptides Inhibiting the Interaction between Neuropilin-1 and Vascular Endothelial Growth Factor-165. Molecules 2019; 24:molecules24091756. [PMID: 31064153 PMCID: PMC6539594 DOI: 10.3390/molecules24091756] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/03/2019] [Accepted: 05/04/2019] [Indexed: 12/11/2022] Open
Abstract
Inhibiting the interaction of neuropilin-1 (NRP-1) with vascular endothelial growth factor (VEGF) has become an interesting mechanism for potential anticancer therapies. In our previous works, we have obtained several submicromolar inhibitors of this interaction, including branched pentapeptides of general structure Lys(Har)-Xxx-Xxx-Arg. With the intent to improve the proteolytic stability of our inhibitors, we turned our attention to 1,4-disubstituted 1,2,3-triazoles as peptide bond isosteres. In the present contribution, we report the synthesis of 23 novel triazolopeptides along with their inhibitory activity. The compounds were synthesized using typical peptide chemistry methods, but with a conversion of amine into azide completely on solid support. The inhibitory activity of the synthesized derivatives spans from 9.2% to 58.1% at 10 μM concentration (the best compound Lys(Har)-GlyΨ[Trl]GlyΨ[Trl]Arg, 3, IC50 = 8.39 μM). Synthesized peptidotriazoles were tested for stability in human plasma and showed remarkable resistance toward proteolysis, with half-life times far exceeding 48 h. In vitro cell survival test resulted in no significant impact on bone marrow derived murine cells 32D viability. By means of molecular dynamics, we were able to propose a binding mode for compound 3 and discuss the observed structure–activity relationships.
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Affiliation(s)
| | - Piotr F J Lipiński
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland.
| | - Anna K Puszko
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Dagmara Tymecka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Beata Wilenska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Wioleta Dudka
- Laboratory of Cytometry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Pasteura 3, 02-093 Warsaw, Poland.
| | - Gerard Y Perret
- Université Paris 13, Sorbonne Paris Cité, INSERM U1125, 74 rue Marcel Cachin, 93017 Bobigny, France.
| | - Rafal Wieczorek
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Aleksandra Misicka
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Department of Neuropeptides, Mossakowski Medical Research Centre, Polish Academy of Sciences, Pawinskiego 5, 02-106 Warsaw, Poland.
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16
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Puszko AK, Sosnowski P, Tymecka D, Raynaud F, Hermine O, Lepelletier Y, Misicka A. Neuropilin-1 peptide-like ligands with proline mimetics, tested using the improved chemiluminescence affinity detection method. MEDCHEMCOMM 2019; 10:332-340. [PMID: 30881620 PMCID: PMC6390686 DOI: 10.1039/c8md00537k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 12/20/2018] [Indexed: 12/31/2022]
Abstract
Many reports have suggested that NRP-1 acts as a co-receptor for VEGF-A165 and boosts tumour growth and metastasis. This NRP-1, due to its important role in tumour progression, triggered interest in the design of new molecules able to significantly inhibit NRP-1/VEGF-A165 interaction to suppress pathological angiogenesis. Our previous SAR studies of compounds, showing affinity for NRP-1, led us to develop branched peptides with general formula Lys(hArg)-AA2-AA3-Arg. Here, three series of analogues were synthesized, in which the middle fragment (AA2 and/or AA3) of initial sequences was substituted with unnatural Pro analogues with different rigidities and ring sizes. The synthesized compounds were screened for VEGF-A165 inhibitory activity on an improved assay (ELISA), which was selected based on our comparative inhibition study of the parent compounds, indicating that the method with chemiluminescence detection gives more accurate data. The results of affinity for NRP-1 and enzymatic stability of newly obtained compounds enabled the selection of new structures, showing a 2 and 4-fold lower IC50 value compared to parent peptides.
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Affiliation(s)
- Anna K Puszko
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ;
| | - Piotr Sosnowski
- Department of Neuropeptides , Mossakowski Medical Research Centre , Polish Academy of Sciences , Pawinskiego 5 , 02-106 Warsaw , Poland
| | - Dagmara Tymecka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ;
| | - Françoise Raynaud
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France
- Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France
- CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Olivier Hermine
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France
- Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France
- CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Yves Lepelletier
- Imagine Institute , Paris Descartes University-Sorbonne Paris Cité , 24 boulevard Montparnasse , 75015 Paris , France
- Laboratory of Cellular and Molecular Basis of Normal Hematopoiesis and Hematological Disorders: Therapeutical Implications , INSERM UMR 1163 , 24 boulevard Montparnasse , 75015 Paris , France
- CNRS ERL 8254 , 24 boulevard Montparnasse , 75015 Paris , France
| | - Aleksandra Misicka
- Faculty of Chemistry , University of Warsaw , Pasteura 1 , 02-093 Warsaw , Poland . ;
- Department of Neuropeptides , Mossakowski Medical Research Centre , Polish Academy of Sciences , Pawinskiego 5 , 02-106 Warsaw , Poland
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17
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Peng K, Bai Y, Zhu Q, Hu B, Xu Y. Targeting VEGF–neuropilin interactions: a promising antitumor strategy. Drug Discov Today 2019; 24:656-664. [PMID: 30315890 DOI: 10.1016/j.drudis.2018.10.004] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 09/26/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023]
Affiliation(s)
- Kewen Peng
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Ying Bai
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Qihua Zhu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
| | - Bin Hu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Yungen Xu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China; Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China.
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18
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Branched pentapeptides as potent inhibitors of the vascular endothelial growth factor 165 binding to Neuropilin-1: Design, synthesis and biological activity. Eur J Med Chem 2018; 158:453-462. [DOI: 10.1016/j.ejmech.2018.08.083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/10/2018] [Accepted: 08/28/2018] [Indexed: 12/31/2022]
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19
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Mota F, Fotinou C, Rana RR, Chan AWE, Yelland T, Arooz MT, O'Leary AP, Hutton J, Frankel P, Zachary I, Selwood D, Djordjevic S. Architecture and hydration of the arginine-binding site of neuropilin-1. FEBS J 2018; 285:1290-1304. [PMID: 29430837 PMCID: PMC5947257 DOI: 10.1111/febs.14405] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 01/26/2018] [Accepted: 02/06/2018] [Indexed: 12/15/2022]
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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Affiliation(s)
- Filipa Mota
- Magnus Life, Magnus Life Science, London, UK
| | | | | | - A W Edith Chan
- Wolfson Institute for Biomedical Research, University College London, UK
| | | | - Mohamed T Arooz
- The Institute of Structural and Molecular Biology, University College London, UK
| | | | | | - Paul Frankel
- Magnus Life, Magnus Life Science, London, UK.,Centre for Cardiovascular Biology & Medicine, BHF Laboratories at University College London, UK
| | - Ian Zachary
- Centre for Cardiovascular Biology & Medicine, BHF Laboratories at University College London, UK
| | - David Selwood
- Wolfson Institute for Biomedical Research, University College London, UK
| | - Snezana Djordjevic
- The Institute of Structural and Molecular Biology, University College London, UK
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