1
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Di Stasi R, De Rosa L, D'Andrea LD. Structure-Based Design of Peptides Targeting VEGF/VEGFRs. Pharmaceuticals (Basel) 2023; 16:851. [PMID: 37375798 DOI: 10.3390/ph16060851] [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: 03/14/2023] [Revised: 05/03/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Vascular endothelial growth factor (VEGF) and its receptors (VEGFRs) play a main role in the regulation of angiogenesis and lymphangiogenesis. Furthermore, they are implicated in the onset of several diseases such as rheumatoid arthritis, degenerative eye conditions, tumor growth, ulcers and ischemia. Therefore, molecules able to target the VEGF and its receptors are of great pharmaceutical interest. Several types of molecules have been reported so far. In this review, we focus on the structure-based design of peptides mimicking VEGF/VEGFR binding epitopes. The binding interface of the complex has been dissected and the different regions challenged for peptide design. All these trials furnished a better understanding of the molecular recognition process and provide us with a wealth of molecules that could be optimized to be exploited for pharmaceutical applications.
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Affiliation(s)
| | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, 80131 Napoli, Italy
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2
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Bechtler C, Lamers C. Macrocyclization strategies for cyclic peptides and peptidomimetics. RSC Med Chem 2021; 12:1325-1351. [PMID: 34447937 PMCID: PMC8372203 DOI: 10.1039/d1md00083g] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/01/2021] [Indexed: 12/12/2022] Open
Abstract
Peptides are a growing therapeutic class due to their unique spatial characteristics that can target traditionally "undruggable" protein-protein interactions and surfaces. Despite their advantages, peptides must overcome several key shortcomings to be considered as drug leads, including their high conformational flexibility and susceptibility to proteolytic cleavage. As a general approach for overcoming these challenges, macrocyclization of a linear peptide can usually improve these characteristics. Their synthetic accessibility makes peptide macrocycles very attractive, though traditional synthetic methods for macrocyclization can be challenging for peptides, especially for head-to-tail cyclization. This review provides an updated summary of the available macrocyclization chemistries, such as traditional lactam formation, azide-alkyne cycloadditions, ring-closing metathesis as well as unconventional cyclization reactions, and it is structured according to the obtained functional groups. Keeping peptide chemistry and screening in mind, the focus is given to reactions applicable in solution, on solid supports, and compatible with contemporary screening methods.
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Affiliation(s)
- Clément Bechtler
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
| | - Christina Lamers
- Department Pharmaceutical Sciences, University of Basel Klingelbergstr. 50 4056 Basel Switzerland
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3
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Wendt M, Bellavita R, Gerber A, Efrém NL, van Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez-Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β-Sheet Mimetics that Target the Transcriptional Coactivator β-Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021; 60:13937-13944. [PMID: 33783110 PMCID: PMC8252567 DOI: 10.1002/anie.202102082] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 12/29/2022]
Abstract
Protein complexes are defined by the three-dimensional structure of participating binding partners. Knowledge about these structures can facilitate the design of peptidomimetics which have been applied for example, as inhibitors of protein-protein interactions (PPIs). Even though β-sheets participate widely in PPIs, they have only rarely served as the basis for peptidomimetic PPI inhibitors, in particular when addressing intracellular targets. Here, we present the structure-based design of β-sheet mimetics targeting the intracellular protein β-catenin, a central component of the Wnt signaling pathway. Based on a protein binding partner of β-catenin, a macrocyclic peptide was designed and its crystal structure in complex with β-catenin obtained. Using this structure, we designed a library of bicyclic β-sheet mimetics employing a late-stage diversification strategy. Several mimetics were identified that compete with transcription factor binding to β-catenin and inhibit Wnt signaling in cells. The presented design strategy can support the development of inhibitors for other β-sheet-mediated PPIs.
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Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nina-Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Thirza van Ramshorst
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Nicholas M Pearce
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Paul R J Davey
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Isabel Everard
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | | | | | - Paolo Grieco
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, The Netherlands
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4
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De Rosa L, Capasso D, Diana D, Stefania R, Di Stasi R, Fattorusso R, D'Andrea LD. Metabolic and conformational stabilization of a VEGF-mimetic beta-hairpin peptide by click-chemistry. Eur J Med Chem 2021; 222:113575. [PMID: 34130005 DOI: 10.1016/j.ejmech.2021.113575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 04/30/2021] [Accepted: 05/19/2021] [Indexed: 01/09/2023]
Abstract
HPLW is a Vascular Endothelial Growth Factor (VEGF)-mimicking beta-hairpin peptide endowed of proangiogenic effect and showing valuable biomedical application in the proangiogenic therapy. However, the translational potential of HPLW is limited by its low metabolic stability, which would shorten the in vivo efficacy of the molecule. Here, we developed a peptide analog of HPLW, named HPLW2, that retains the structural and biological properties of the original peptide but features an impressive resistance to degradation by human serum proteases. HPLW2 was obtained by covalently modifying the chemical structure of the peptide with molecular tools known to impart protease resistance. Notably, the peptide was cyclized by installing an interstrand triazole bridge through Cu(I)-catalyzed azide-alkyne 1,3-dipolar cycloaddition (CuAAC) reaction. HPLW2 appears as a novel and promising drug candidate with potential biomedical application in the proangiogenic therapy as a low molecular weight drug, alternative to the use of VEGF. Our work points out the utility of the interstrand triazole bridge as effective chemical platform for the conformational and metabolic stabilization of beta-hairpin bioactive peptides.
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Affiliation(s)
- Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Domenica Capasso
- CESTEV, Università di Napoli "Federico II", Via De Amicis 95, 80134, Napoli, Italy; CIRPeB Università di Napoli "Federico II" Via Mezzocannone 16, 80134, Napoli, Italy
| | - Donatella Diana
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Rachele Stefania
- Dipartimento di Biotecnologie Molecolari e Scienze per La Salute, Università di Torino, Via Nizza 52, 10126, Torino, Italy
| | - Rossella Di Stasi
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, 80134, Napoli, Italy
| | - Roberto Fattorusso
- CIRPeB Università di Napoli "Federico II" Via Mezzocannone 16, 80134, Napoli, Italy; Dipartimento di Scienze e Tecnologie Ambientali, Biologiche e Farmaceutiche, Università Della Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy
| | - Luca Domenico D'Andrea
- Istituto di Scienze e Tecnologie Chimiche "Giulio Natta", CNR, Via M. Bianco 9, 20131, Milano, Italy.
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5
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Wendt M, Bellavita R, Gerber A, Efrém N, Ramshorst T, Pearce NM, Davey PRJ, Everard I, Vazquez‐Chantada M, Chiarparin E, Grieco P, Hennig S, Grossmann TN. Bicyclic β‐Sheet Mimetics that Target the Transcriptional Coactivator β‐Catenin and Inhibit Wnt Signaling. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202102082] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Mathias Wendt
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Rosa Bellavita
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Alan Gerber
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nina‐Louisa Efrém
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Thirza Ramshorst
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Nicholas M. Pearce
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | | | - Isabel Everard
- Mechanistic Biology and Profiling Discovery Sciences, R&D AstraZeneca Cambridge UK
| | | | | | - Paolo Grieco
- Department of Pharmacy University of Naples Federico II Naples Italy
| | - Sven Hennig
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
| | - Tom N. Grossmann
- Department of Chemistry and Pharmaceutical Sciences VU University Amsterdam Amsterdam The Netherlands
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6
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Abstract
This Review is devoted to the chemistry of macrocyclic peptides having heterocyclic fragments in their structure. These motifs are present in many natural products and synthetic macrocycles designed against a particular biochemical target. Thiazole and oxazole are particularly common constituents of naturally occurring macrocyclic peptide molecules. This frequency of occurrence is because the thiazole and oxazole rings originate from cysteine, serine, and threonine residues. Whereas other heteroaryl groups are found less frequently, they offer many insightful lessons that range from conformational control to receptor/ligand interactions. Many options to develop new and improved technologies to prepare natural products have appeared in recent years, and the synthetic community has been pursuing synthetic macrocycles that have no precedent in nature. This Review attempts to summarize progress in this area.
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Affiliation(s)
- Ivan V Smolyar
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada
| | - Valentine G Nenajdenko
- Department of Chemistry , Moscow State University , Leninskije Gory , 199991 Moscow , Russia
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7
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Stefanucci A, Lei W, Pieretti S, Novellino E, Dimmito MP, Marzoli F, Streicher JM, Mollica A. On resin click-chemistry-mediated synthesis of novel enkephalin analogues with potent anti-nociceptive activity. Sci Rep 2019; 9:5771. [PMID: 30962495 PMCID: PMC6453917 DOI: 10.1038/s41598-019-42289-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 03/20/2019] [Indexed: 11/22/2022] Open
Abstract
Here, we report the chemical synthesis of two DPDPE analogues 7a (NOVA1) and 7b (NOVA2). This entailed the solid-phase synthesis of two enkephalin precursor chains followed by a CuI-catalyzed azide-alkyne cycloaddition, with the aim of improving in vivo analgesic efficacy versus DPDPE. NOVA2 showed good affinity and selectivity for the μ-opioid receptor (KI of 59.2 nM, EC50 of 12.9 nM, EMax of 87.3%), and long lasting anti-nociceptive effects in mice when compared to DPDPE.
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Affiliation(s)
- Azzurra Stefanucci
- Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio", Via dei Vestini 31, 66100, Chieti, Italy
| | - Wei Lei
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Stefano Pieretti
- Istituto Superiore di Sanità, Centro Nazionale Ricerca e Valutazione Preclinica e Clinica dei farmaci, Viale Regina Elena 299, 00161, Rome, Italy
| | - Ettore Novellino
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, 80131, Naples, Italy
| | - Marilisa Pia Dimmito
- Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio", Via dei Vestini 31, 66100, Chieti, Italy
| | - Francesca Marzoli
- Istituto Superiore di Sanità, Centro Nazionale Ricerca e Valutazione Preclinica e Clinica dei farmaci, Viale Regina Elena 299, 00161, Rome, Italy
| | - John M Streicher
- Department of Pharmacology, College of Medicine, University of Arizona, Tucson, AZ, USA
| | - Adriano Mollica
- Dipartimento di Farmacia, Università di Chieti-Pescara "G. d'Annunzio", Via dei Vestini 31, 66100, Chieti, Italy.
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8
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Hu H, Kofoed C, Li M, Gonçalves JP, Hansen J, Wolfram M, Hansen AK, Friis Hansen CH, Diness F, Schoffelen S, Meldal M. Computational Evolution of Threonine-Rich β-Hairpin Peptides Mimicking Specificity and Affinity of Antibodies. ACS CENTRAL SCIENCE 2019; 5:259-269. [PMID: 30834314 PMCID: PMC6396188 DOI: 10.1021/acscentsci.8b00614] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Indexed: 05/07/2023]
Abstract
The development of recognition molecules with antibody-like properties is of great value to the biotechnological and bioanalytical communities. The recognition molecules presented here are peptides with a strong tendency to form β-hairpin structures, stabilized by alternate threonines, which are located at one face of the peptide. Amino acids at the other face of the peptide are available for interaction with the target molecule. Using this scaffold, we demonstrate that recognition molecules can efficiently be designed in silico toward four structurally unrelated proteins, GFP, IL-1β, IL-2, and IL-6. On solid support, 10 different antibody-mimetic recognition molecules were synthesized. They displayed high affinity and no cross-reactivity, as observed by fluorescence microscopy. Stabilized variants were readily obtained by incorporation of azido acids and propargylglycine followed by cyclization via the Cu(I)-catalyzed alkyne-azide cycloaddition reaction. As this new class of antibody mimics can be designed toward essentially any protein, the concept is believed to be useful to a wide range of technologies. Here, their use in protein separation and in the detection of proteins in a sandwich-type assay is demonstrated.
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9
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Design and structural characterisation of monomeric water-soluble α-helix and β-hairpin peptides: State-of-the-art. Arch Biochem Biophys 2019; 661:149-167. [DOI: 10.1016/j.abb.2018.11.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 11/06/2018] [Accepted: 11/14/2018] [Indexed: 02/06/2023]
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10
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Diana D, Di Salvo C, Celentano V, De Rosa L, Romanelli A, Fattorusso R, D'Andrea LD. Conformational stabilization of a β-hairpin through a triazole–tryptophan interaction. Org Biomol Chem 2018; 16:787-795. [DOI: 10.1039/c7ob02815f] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Triazole and indole rings stabilize a β-hairpin conformation through an aromatic–aromatic interaction.
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Affiliation(s)
| | | | | | - Lucia De Rosa
- Istituto di Biostrutture e Bioimmagini
- CNR
- Napoli
- Italy
| | | | - Roberto Fattorusso
- Dipartimento di Scienze e Tecnologie Ambientali
- Biologiche e Farmaceutiche
- Università della Campania “L. Vanvitelli”
- Caserta
- Italy
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11
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Andersson H, Danelius E, Jarvoll P, Niebling S, Hughes AJ, Westenhoff S, Brath U, Erdélyi M. Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar β-Hairpins. ACS OMEGA 2017; 2:508-516. [PMID: 28261689 PMCID: PMC5331454 DOI: 10.1021/acsomega.6b00484] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 01/16/2017] [Indexed: 05/20/2023]
Abstract
We have evaluated the ability of nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopies to describe the difference in the folding propensities of two structurally highly similar cyclic β-hairpins, comparing the outcome to that of molecular dynamics simulations. NAMFIS-type NMR ensemble analysis and CD spectroscopy were observed to accurately describe the consequence of altering a single interaction site, whereas a single-site 13C NMR chemical shift melting curve-based technique was not.
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Affiliation(s)
- Hanna Andersson
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Emma Danelius
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Patrik Jarvoll
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Stephan Niebling
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Ashley J. Hughes
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Ulrika Brath
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
| | - Máté Erdélyi
- Department
of Chemistry and Molecular Biology, University
of Gothenburg, Kemivägen 10, SE-412 96 Gothenburg, Sweden
- The
Swedish NMR Centre, Medicinaregatan
5c, SE-413 96 Gothenburg, Sweden
- E-mail: (M.E.)
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