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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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2
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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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3
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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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4
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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: 9.0] [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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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: 6] [Impact Index Per Article: 3.0] [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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6
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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: 26] [Impact Index Per Article: 8.7] [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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7
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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: 4] [Impact Index Per Article: 1.0] [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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8
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Berlinck RGS, Bernardi DI, Fill T, Fernandes AAG, Jurberg ID. The chemistry and biology of guanidine secondary metabolites. Nat Prod Rep 2020; 38:586-667. [PMID: 33021301 DOI: 10.1039/d0np00051e] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: 2017-2019Guanidine natural products isolated from microorganisms, marine invertebrates and terrestrial plants, amphibians and spiders, represented by non-ribosomal peptides, guanidine-bearing polyketides, alkaloids, terpenoids and shikimic acid derived, are the subject of this review. The topics include the discovery of new metabolites, total synthesis of natural guanidine compounds, biological activity and mechanism-of-action, biosynthesis and ecological functions.
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Affiliation(s)
- Roberto G S Berlinck
- Instituto de Química de São Carlos, Universidade de São Paulo, CP 780, CEP 13560-970, São Carlos, SP, Brazil.
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9
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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: 3.3] [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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10
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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: 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: 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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11
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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: 41] [Impact Index Per Article: 8.2] [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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12
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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 DOI: 10.1039/c8md00537k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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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13
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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: 3.5] [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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14
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Fatino A, Baca G, Weeramange C, Rafferty RJ. Total Synthesis of Reniochalistatin E. JOURNAL OF NATURAL PRODUCTS 2017; 80:3234-3240. [PMID: 29220182 DOI: 10.1021/acs.jnatprod.7b00656] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Reniochalistatin E (1) is one of the five related cyclic peptides isolated from the marine sponge Reniochalina stalagmitis. The discovery of these compounds resulted from a screening program directed toward the identification of proline-rich bioactive compounds. Reniochalistatin E is the only member of the family to possess a tryptophan amino acid residue. Given the cytotoxicity observed for 1, efforts were directed toward developing a synthetic route to 1. The first total synthesis of 1 has been accomplished in a 15-step route in an overall 5.0% yield. The synthetic sample of reniochalistatin E was shown to have similar activity toward HeLa and RPMI-8226 cell lines compared to the natural sample, with IC50 values of 16.9 vs 17.3 μM and 4.5 vs 4.9 μM, respectively. Interestingly, both of the fully deprotected octapeptides constructed toward the synthesis of reniochalistatin E were shown to have cytotoxicity. The route provides a means to probe the structure-activity relationship of 1 and further biological investigations.
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Affiliation(s)
- Anthony Fatino
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
| | - Giovanna Baca
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
| | - Chamitha Weeramange
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
| | - Ryan J Rafferty
- Department of Chemistry, Kansas State University , Manhattan, Kansas 66506, United States
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