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Hamers SMWR, Boyle AL, Sharp TH. Engineering Agonistic Bispecifics to Investigate the Influence of Distance on Surface-Mediated Complement Activation. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2024; 213:235-243. [PMID: 38819221 PMCID: PMC11215631 DOI: 10.4049/jimmunol.2400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 05/12/2024] [Indexed: 06/01/2024]
Abstract
The development of agonists capable of activating the human complement system by binding to the C1 complex presents a novel approach for targeted cell killing. Bispecific nanobodies and Abs can successfully use C1 for this purpose; however, efficacy varies significantly between epitopes, Ab type, and bispecific design. To address this variability, we investigated monomeric agonists of C1 in the form of bispecific nanobodies, which lack Fc domains that lead to oligomerization in Abs. These therefore offer an ideal opportunity to explore the geometric parameters crucial for C1 activation. In this study, we explored the impact of linker length as a metric for Ag and epitope location. DNA nanotechnology and protein engineering allowed us to design linkers with controlled lengths and flexibilities, revealing a critical range of end-to-end distances for optimal complement activation. We discovered that differences in complement activation were not caused by differential C1 activation or subsequent cleavage of C4, but instead impacted C4b deposition and downstream membrane lysis. Considering the importance of Ab class and subclass, this study provides insights into the structural requirements of C1 binding and activation, highlighting linker and hinge engineering as a potential strategy to enhance potency over specific cellular targets. Additionally, using DNA nanotechnology to modify geometric parameters demonstrated the potential for synthetic biology in complement activation. Overall, this research offers valuable insights into the design and optimization of agonists for targeted cell killing through complement activation.
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Affiliation(s)
| | - Aimee L. Boyle
- Leiden Institute of Chemistry, Leiden University, Leiden, the Netherlands
- School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Thomas H. Sharp
- Department of Cell and Chemical Biology, Leiden University Medical Centre, Leiden, the Netherlands
- School of Biochemistry, University of Bristol, Bristol, United Kingdom
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2
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Gaikwad V, Choudhury AR, Chakrabarti R. Decoding the dynamics of BCL9 triazole stapled peptide. Biophys Chem 2024; 307:107197. [PMID: 38335808 DOI: 10.1016/j.bpc.2024.107197] [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: 10/13/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
BCL9 is a key protein in Wnt signaling pathway. It acts as a transcriptional co-activator to β-catenin, and dysregulation in this pathway leads to tumor growth. Inhibiting such a protein-protein interaction is considered as a therapeutic challenge. The interaction between β-catenin and BCL9 is facilitated by a 23-residue helical domain from BCL9 and a hydrophobic groove of β-catenin. To prevent this interaction, a peptide that mimics the alpha-helical domain of BCL9 can be designed. Stapling is considered a successful strategy in the pursuit of designing such peptides in which amino acids side are stitched together using chemical moieties. Among the various types of cross-linkers, triazole is the most rapid and effective one synthesized via click reaction. However, the underlying interactions behind maintaining the secondary structure of stapled peptides remain less explored. In the current work, we employed the molecular dynamics simulation to study the conformational behavior of the experimentally synthesized single and double triazole stapled BCL9 peptide. Upon the addition of a triazole staple, there is a significant reduction in the conformational space of BCL9. The helical character of the stapled peptide increases with an increase in separation between the triazole cross-linkers. Also, we encompassed the Replica Exchange with Solute Tempering (REST2) simulation to validate the high-temperature response of the stapled peptide. From REST2, the PCA and t-SNE show the reduction in distinct cluster formation on the addition of triazole staple. Our study infers further development of these triazole-stapled BCL9 peptides into effective inhibitors to target the interaction between β-catenin and BCL9.
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Affiliation(s)
- Vikram Gaikwad
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Asha Rani Choudhury
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Rajarshi Chakrabarti
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
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3
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Singh H, Chenna A, Gangwar U, Borah J, Goel G, Haridas V. Bispidine as a β-strand nucleator: from a β-arch to self-assembled cages and vesicles. Chem Sci 2021; 12:15757-15764. [PMID: 35003608 PMCID: PMC8654037 DOI: 10.1039/d1sc04860k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 10/25/2021] [Indexed: 12/23/2022] Open
Abstract
The development of synthetic scaffolds that nucleate well-folded secondary structures is highly challenging. Herein, we designed and synthesized a series of core-modified peptides (F1, F2, F3, and F4) that fold into β-strand structures. These bispidine-scaffolded peptides were studied by CD, IR, NMR, single crystal XRD, and Molecular Dynamics (MD) simulations to investigate their conformational preferences. Solid-state and solution studies revealed that bispidine is a versatile scaffold that could be placed either at the terminal or at the middle of the peptide strand for nucleating the β-strand structure. Scaffolds that nucleate an isolated β-strand conformation are rare. Bispidine placed at the C-terminus of the peptide chain could nucleate a β-strand conformation, while bispidine placed at the middle resulted in a β-arch conformation. This nucleation activity stems from the ability to restrict the psi torsion angle (ψ) through intramolecular C5 hydrogen bonding between the equatorial hydrogen(s) of bispidine and the carbonyl oxygen(s) of the amino acid close to the scaffold. Furthermore, the bispidine peptidomimetic with a super secondary structure, namely β-arch, assembled into single-hole submicron cages and spherical vesicles as evident from microscopic studies. The design logic defined here will be a significant strategy for the development of β-strand mimetics and super secondary structures.
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Affiliation(s)
- Hanuman Singh
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Akshay Chenna
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Upanshu Gangwar
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Julie Borah
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - Gaurav Goel
- Department of Chemical Engineering, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
| | - V Haridas
- Department of Chemistry, Indian Institute of Technology Delhi Hauz Khas New Delhi-110016 India
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4
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D'Ercole A, Sabatino G, Pacini L, Impresari E, Capecchi I, Papini AM, Rovero P. On‐resin microwave‐assisted copper‐catalyzed azide‐alkyne cycloaddition of H1‐relaxin B single chain ‘stapled’ analogues. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24159] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Annunziata D'Ercole
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- FIS Fabbrica Italiana Sintetici S.p.A Vicenza Italy
| | - Giuseppina Sabatino
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- CNR‐IC Istituto di Cristallografia Catania Italy
| | | | - Elisa Impresari
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
| | - Ilaria Capecchi
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
| | - Anna Maria Papini
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Chemistry ‘Ugo Schiff’University of Florence Sesto Fiorentino Italy
- CNR‐IC Istituto di Cristallografia Catania Italy
- PeptLab@UCP and Laboratory of Chemical Biology EA4505CY Cergy Paris University Cergy‐Pontoise France
| | - Paolo Rovero
- CNR‐IC Istituto di Cristallografia Catania Italy
- Laboratory of Peptide and Protein Chemistry and Biology, Department of Neurosciences, Psychology, Drug Research and Child Health—Section of Pharmaceutical Sciences and NutraceuticsUniversity of Florence Sesto Fiorentino Italy
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5
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Kulikov OV, Sevryugina YV, Mehmood A, Saraogi I. Characterization of aggregated morphologies derived from mono- and bis-arylbenzamides – potential alpha-helix mimetics. NEW J CHEM 2017. [DOI: 10.1039/c6nj03775e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report here the synthesis and self-assembly studies of a family of benzamide backbone oligomers bearing various alkyl side chains (e.g., isopropyl, isobutyl, and 2-ethylpentyl), which are potential alpha-helix mimetics capable of disrupting protein–protein interactions.
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Affiliation(s)
- Oleg V. Kulikov
- Department of Chemistry
- Massachusetts Institute of Technology
- Cambridge
- USA
| | | | - Arshad Mehmood
- Department of Chemistry
- Texas Christian University
- Fort Worth
- USA
| | - Ishu Saraogi
- Department of Chemistry
- Indian Institute of Science Education and Research Bhopal
- Bhopal 462066
- India
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6
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Maffucci I, Clayden J, Contini A. Origin of Helical Screw Sense Selectivity Induced by Chiral Constrained Cα-Tetrasubstituted α-Amino Acids in Aib-based Peptides. J Phys Chem B 2015; 119:14003-13. [PMID: 26457452 DOI: 10.1021/acs.jpcb.5b07050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The mechanisms behind the propensity of chiral constrained Cα-tetrasubstituted amino acids (cCTAAs) to induce one particular helical screw sense, when included in the Ac-Aib2-cCTAA-Aib2-NHMe peptide model, were studied through replica exchange molecular dynamics, potential of mean force, and quantum theory of atoms in molecules calculations. We observed that cCTAAs exert their effect on helical screw sense selectivity through the positioning of the side chain to generate steric hindrance in either the (-x, +y, +z) or (+x, +y, -z) sectors of a right-handed 3D Cartesian space, where the z axis corresponds to the axis of the helix and the Cα lies on the +y semiaxis (0, +y, 0). The different strengthening of the noncovalent interactions, also comprising C-H···O interactions, exerted by the cCTAA in the right-handed or left-handed helix was also found important to define the preference of a cCTAA for a particular helix screw sense.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
| | - Jonathan Clayden
- School of Chemistry, University of Manchester , Oxford Road, Manchester M13 9PL, U.K
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche - Sezione di Chimica Generale e Organica "Alessandro Marchesini", Università degli Studi di Milano , Via Venezian, 21, 20133 Milano, Italy
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7
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Lau YH, de Andrade P, Wu Y, Spring DR. Peptide stapling techniques based on different macrocyclisation chemistries. Chem Soc Rev 2014; 44:91-102. [PMID: 25199043 DOI: 10.1039/c4cs00246f] [Citation(s) in RCA: 408] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Peptide stapling is a strategy for constraining short peptides typically in an alpha-helical conformation. Stapling is carried out by covalently linking the side-chains of two amino acids, thereby forming a peptide macrocycle. There is an expanding repertoire of stapling techniques based on different macrocyclisation chemistries. In this tutorial review, we categorise and analyse key examples of peptide stapling in terms of their synthesis and applicability to biological systems.
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Affiliation(s)
- Yu Heng Lau
- University Chemical Laboratory, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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8
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de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014; 53:6965-9. [DOI: 10.1002/anie.201310245] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 03/10/2014] [Indexed: 11/09/2022]
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9
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de Araujo AD, Hoang HN, Kok WM, Diness F, Gupta P, Hill TA, Driver RW, Price DA, Liras S, Fairlie DP. Comparative α-Helicity of Cyclic Pentapeptides in Water. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310245] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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10
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Mazzier D, Peggion C, Toniolo C, Moretto A. Enhancement of the helical content and stability induced in a linear oligopeptide by ani, i+4 intramolecularly double stapled, overlapping, bicyclic [31, 22, 5]-(E)ene motif. Biopolymers 2014; 102:115-23. [DOI: 10.1002/bip.22438] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2013] [Revised: 08/28/2013] [Accepted: 10/11/2013] [Indexed: 11/05/2022]
Affiliation(s)
- Daniela Mazzier
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Cristina Peggion
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Claudio Toniolo
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
| | - Alessandro Moretto
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova; 35131 Padova Italy
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11
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Góngora-Benítez M, Tulla-Puche J, Albericio F. Multifaceted Roles of Disulfide Bonds. Peptides as Therapeutics. Chem Rev 2013; 114:901-26. [DOI: 10.1021/cr400031z] [Citation(s) in RCA: 388] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Miriam Góngora-Benítez
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Judit Tulla-Puche
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
| | - Fernando Albericio
- Institute
for Research in Biomedicine (IRB Barcelona), Barcelona, 08028 Spain
- CIBER-BBN, Barcelona Science
Park, Barcelona, 08028 Spain
- Department
of Organic Chemistry, University of Barcelona, Barcelona, 08028 Spain
- School of Chemistry & Physics, University of KwaZulu-Natal, 4001 Durban, South Africa
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12
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Naduthambi D, Bhor S, Elbaum MB, Zondlo NJ. Synthesis of a tetrasubstituted tetrahydronaphthalene scaffold for α-helix mimicry via a MgBr2-catalyzed Friedel-Crafts epoxide cycloalkylation. Org Lett 2013; 15:4892-5. [PMID: 24016333 DOI: 10.1021/ol402334j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
α-Helices are ubiquitous protein recognition elements that bind diverse biomolecular targets. The synthesis of a small molecule scaffold to present the side chains of an α-helix is described. The 1,3,5,7-tetrasubstituted 1,2,3,4-tetrahydronaphthalene scaffold, providing mimicry of the i, i+3, and i+4 positions of an α-helix, was synthesized using a novel MgBr2-catalyzed Friedel-Crafts epoxide cycloalkylation as the key step. Each position may be differentiated via O-alkylation after scaffold synthesis, generating a diversity-oriented approach to readily synthesize proteomimetics for different targets.
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Affiliation(s)
- Devan Naduthambi
- Department of Chemistry and Biochemistry, University of Delaware , Newark, Delaware 19716, United States
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13
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Bayly AR, White AJP, Spivey AC. Design and Synthesis of a Prototype Scaffold for Five-Residue α-Helix Mimetics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300478] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Haney CM, Horne WS. Oxime side-chain cross-links in an α-helical coiled-coil protein: structure, thermodynamics, and folding-templated synthesis of bicyclic species. Chemistry 2013; 19:11342-51. [PMID: 23843311 DOI: 10.1002/chem.201300506] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Indexed: 01/11/2023]
Abstract
Covalent side-chain cross-links are a versatile method to control peptide folding, particularly when α-helical secondary structure is the target. Here, we examine the application of oxime bridges, formed by the chemoselective reaction between aminooxy and aldehyde side chains, for the stabilization of a helical peptide involved in a protein-protein complex. A series of sequence variants of the dimeric coiled coil GCN4-p1 bearing oxime bridges at solvent-exposed positions were prepared and biophysically characterized. Triggered unmasking of a side-chain aldehyde in situ and subsequent cyclization proceed rapidly and cleanly at pH 7 in the folded protein complex. Comparison of folding thermodynamics among a series of different oxime bridges show that the cross links are consistently stabilizing to the coiled coil, with the extent of stabilization sensitive to the exact size and structure of the macrocycle. X-ray crystallographic analysis of a coiled coil with the best cross link in place and a second structure of its linear precursor show how the bridge is accommodated into an α-helix. Preparation of a bicyclic oligomer by simultaneous formation of two linkages in situ demonstrates the potential use of triggered oxime formation to both trap and stabilize a particular peptide folded conformation in the bound state.
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Affiliation(s)
- Conor M Haney
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260, USA
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15
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Gori A, Longhi R, Peri C, Colombo G. Peptides for immunological purposes: design, strategies and applications. Amino Acids 2013; 45:257-68. [DOI: 10.1007/s00726-013-1526-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 05/24/2013] [Indexed: 12/30/2022]
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16
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Kulikov OV, Thompson S, Xu H, Incarvito CD, Scott RTW, Saraogi I, Nevola L, Hamilton AD. Design and Synthesis of Oligoamide-Based Double α-Helix Mimetics. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300363] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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17
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Hurevich M, Ratner-Hurevich M, Tal-Gan Y, Shalev DE, Ben-Sasson SZ, Gilon C. Backbone cyclic helix mimetic of chemokine (C-C motif) receptor 2: a rational approach for inhibiting dimerization of G protein-coupled receptors. Bioorg Med Chem 2013; 21:3958-66. [PMID: 23706536 DOI: 10.1016/j.bmc.2013.03.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2012] [Revised: 02/28/2013] [Accepted: 03/01/2013] [Indexed: 10/27/2022]
Abstract
The transmembrane helical bundle of G protein-coupled receptors (GPCRs) dimerize through helix-helix interactions in response to inflammatory stimulation. A strategy was developed to target the helical dimerization site of GPCRs by peptidomimetics with drug like properties. The concept was demonstrated by selecting a potent backbone cyclic helix mimetic from a library that derived from the dimerization region of chemokine (C-C motif) receptor 2 (CCR2) that is a key player in Multiple Sclerosis. We showed that CCR2 based backbone cyclic peptide having a stable helix structure inhibits specific CCR2-mediated chemotactic migration.
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Affiliation(s)
- Mattan Hurevich
- Institute of Chemistry, The Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
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18
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Peters M, Trobe M, Tan H, Kleineweischede R, Breinbauer R. A modular synthesis of teraryl-based α-helix mimetics, part 1: Synthesis of core fragments with two electronically differentiated leaving groups. Chemistry 2013; 19:2442-9. [PMID: 23292813 DOI: 10.1002/chem.201203005] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/12/2012] [Indexed: 01/12/2023]
Abstract
Teraryl-based α-helix mimetics have proven to be useful compounds for the inhibition of protein-protein interactions (PPI). We have developed a modular and flexible approach for the synthesis of teraryl-based α-helix mimetics. Central to our strategy is the use of a benzene core unit featuring two leaving groups of differentiated reactivity in the Pd-catalyzed cross-coupling used for terphenyl assembly. With the halogen/diazonium route and the halogen/triflate route, two strategies have successfully been established. The synthesis of core building blocks with aliphatic (Ala, Val, Leu, Ile), aromatic (Phe), polar (Cys, Lys), hydrophilic (Ser, Gln), and acidic (Glu) amino acid side chains are reported.
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Affiliation(s)
- Martin Peters
- Institute of Organic Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
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19
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Haridas V, Sadanandan S, Gopalakrishna MVS, Bijesh MB, Verma RP, Chinthalapalli S, Shandilya A. Bispidine as a helix inducing scaffold: examples of helically folded linear peptides. Chem Commun (Camb) 2013; 49:10980-2. [DOI: 10.1039/c3cc45649h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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20
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Wrobel M, Aubé J, König B. Parallel solid-phase synthesis of diaryltriazoles. Beilstein J Org Chem 2012; 8:1027-36. [PMID: 23019430 PMCID: PMC3458720 DOI: 10.3762/bjoc.8.115] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2012] [Accepted: 06/13/2012] [Indexed: 11/30/2022] Open
Abstract
A series of substituted diaryltriazoles was prepared by a solid-phase-synthesis protocol using a modified Wang resin. The copper(I)- or ruthenium(II)-catalyzed 1,3-cycloaddition on the polymer bead allowed a rapid synthesis of the target compounds in a parallel fashion with in many cases good to excellent yields. Substituted diaryltriazoles resemble a molecular structure similar to established terphenyl-alpha-helix peptide mimics and have therefore the potential to act as selective inhibitors for protein-protein interactions.
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Affiliation(s)
- Matthias Wrobel
- Fakultät für Chemie und Pharmazie, Universität Regensburg, D-93040 Regensburg, Germany, Fax: +49 9419431717
| | - Jeffrey Aubé
- Department of Medicinal Chemistry and the Chemical Methodology and Library Development Center, University of Kansas, Delbert M. Shankel Structural Biology Center, 2121 Simons Drive, West Campus, Lawrence, KS 66047, USA
| | - Burkhard König
- Fakultät für Chemie und Pharmazie, Universität Regensburg, D-93040 Regensburg, Germany, Fax: +49 9419431717
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Prabhakaran P, Azzarito V, Jacobs T, Hardie MJ, Kilner CA, Edwards TA, Warriner SL, Wilson AJ. Conformational properties of O-alkylated benzamides. Tetrahedron 2012. [DOI: 10.1016/j.tet.2011.11.078] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Haridas V, Sadanandan S, Sharma YK, Chinthalapalli S, Shandilya A. Bispidine as a secondary structure nucleator in peptides. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2011.11.112] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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23
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Kawamoto SA, Coleska A, Ran X, Yi H, Yang CY, Wang S. Design of triazole-stapled BCL9 α-helical peptides to target the β-catenin/B-cell CLL/lymphoma 9 (BCL9) protein-protein interaction. J Med Chem 2012; 55:1137-46. [PMID: 22196480 DOI: 10.1021/jm201125d] [Citation(s) in RCA: 196] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction between β-catenin and B-cell CLL/lymphoma 9 (BCL9), critical for the transcriptional activity of β-catenin, is mediated by a helical segment from BCL9 and a large binding groove in β-catenin. Design of potent, metabolically stable BCL9 peptides represents an attractive approach to inhibit the activity of β-catenin. In this study, we report the use of the Huisgen 1,3-dipolar cycloaddition reaction to generate triazole-stapled BCL9 α-helical peptides. The high efficiency and mild conditions of this "click" reaction combined with the ease of synthesis of the necessary unnatural amino acids allows for facile synthesis of triazole-stapled peptides. We have performed extensive optimization of this approach and identified the optimal combinations of azido and alkynyl linkers necessary for stapling BCL9 helices. The unsymmetrical nature of the triazole staple also allowed the synthesis of double-stapled BCL9 peptides, which show a marked increase in helical character and an improvement in binding affinity and metabolic stability relative to wild-type and linear BCL9 peptides. This study lays the foundation for further optimization of these triazole-stapled BCL9 peptides as potent, metabolically stable, and cell-permeable inhibitors to target the β-catenin and BCL9 interaction.
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Affiliation(s)
- Steven A Kawamoto
- Department of Medicinal Chemistry, Comprehensive Cancer Center, University of Michigan, Ann Arbor, Michigan 48109, United States
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Kulikov OV, Hamilton AD. Synthesis of the novel trimeric benzamides—potential inhibitors of protein–protein interactions. RSC Adv 2012. [DOI: 10.1039/c2ra01153k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Howson SE, Bolhuis A, Brabec V, Clarkson GJ, Malina J, Rodger A, Scott P. Optically pure, water-stable metallo-helical ‘flexicate’ assemblies with antibiotic activity. Nat Chem 2011; 4:31-6. [DOI: 10.1038/nchem.1206] [Citation(s) in RCA: 176] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Accepted: 10/17/2011] [Indexed: 01/18/2023]
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26
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Developing potent backbone cyclic peptides bearing the shared epitope sequence as rheumatoid arthritis drug-leads. Bioorg Med Chem Lett 2011; 22:493-6. [PMID: 22113111 DOI: 10.1016/j.bmcl.2011.10.098] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Revised: 10/18/2011] [Accepted: 10/27/2011] [Indexed: 01/06/2023]
Abstract
Rheumatoid arthritis (RA) is a common human leukocyte antigen-associated disease. Most RA patients have a five-residue sequence motif called the shared epitope (SE) in the DRβ-chain of the HLA-DRB1 protein. The SE was found to activate nitric oxide (NO) production, suggesting a possible mechanism for RA development. The native conformation of the SE is presumed to be an α-helix, thus using cyclic peptides to stabilize this conformation may produce a potent SE mimetic which will have drug-like properties. We present the development of a backbone cyclic SE mimetic that activates NO production in the low nM range. Circular dichroism analysis revealed a conformational change from for the parent linear peptides to the cyclic analogs. The most active cyclic analog is completely stable towards trypsin/chymotrypsin degradation while the linear 15-mer analogs completely degraded within 30 min. The outcome of this study is a potent cyclic peptide with drug-like properties that can be used as a template for drug development.
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Hydrophobic side-chain interactions in a family of dimeric amide foldamers-potential alpha-helix mimetics. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Moretto A, Crisma M, Formaggio F, Toniolo C. Building a bridge between peptide chemistry and organic chemistry: intramolecular macrocyclization reactions and supramolecular chemistry with helical peptide substrates. Biopolymers 2011; 94:721-32. [PMID: 20564031 DOI: 10.1002/bip.21445] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In our ongoing efforts to build a bridge between peptide chemistry and organic chemistry, we are currently investigating: (1) two types of intramolecular macrocyclization reactions in 3(10)-helical peptides, and (2) a peptido[2]rotaxane molecular machine as a supramolecular tool using a 3(10)-helical peptide as the axle. More specifically, we studied the following two reactions: (a) the intramolecular ring-closing olefin metathesis between two amino acid residues with side chains bearing an allyl group, and (b) the intramolecular Paternò-Yang photoreaction, using a benzophenone-based amino acid as a photoaffinity reagent for a Met residue. Both reactions involve formation of a new C--C bond. As for the supramolecular system examined, we were able to identify the two stations of a new peptido[2]rotaxane characterized by an -(Aib)(6)- axle and to reversibly switch the aromatic tetramide macrocyclic wheel from one station to the next. This article summarizes the information available in the literature from other groups and the published/unpublished data originated from our laboratory on these research areas.
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Affiliation(s)
- Alessandro Moretto
- Department of Chemistry, Institute of Biomolecular Chemistry, Padova Unit, CNR, Padova 35131, Italy
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29
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Ressurreição ASM, Delatouche R, Gennari C, Piarulli U. Bifunctional 2,5‐Diketopiperazines as Rigid Three‐Dimensional Scaffolds in Receptors and Peptidomimetics. European J Org Chem 2010. [DOI: 10.1002/ejoc.201001330] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Ana Sofia M. Ressurreição
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
- Universidade de Lisboa, iMed. UL, Faculdade de Farmácia, Av. Prof. Gama Pinto, 649‐003 Lisboa, Portugal
| | - Régis Delatouche
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
| | - Cesare Gennari
- Università degli Studi di Milano, Dipartimento di ChimicaOrganica e Industriale, via G. Venezian 21, 20133 Milano, Italy
| | - Umberto Piarulli
- Università degli Studi dell'Insubria, Dipartimento di Scienze Chimiche e Ambientali, via Valleggio 11, 22100 Como, Italy, Fax: +39‐031‐2386449
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Drewry DH, Macarron R. Enhancements of screening collections to address areas of unmet medical need: an industry perspective. Curr Opin Chem Biol 2010; 14:289-98. [PMID: 20413343 DOI: 10.1016/j.cbpa.2010.03.024] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2010] [Revised: 02/19/2010] [Accepted: 03/24/2010] [Indexed: 01/31/2023]
Abstract
The past 20 years have witnessed an impressive expansion of the 'drug space'; defined as the intersection of the Medicinal Chemistry space and the Biologically Active space relevant in the quest for new treatments for disease. Despite the success of known lead discovery tactics, areas of unmet medical need are often linked to challenging or novel targets and are poorly served by current screening collections. A successful strategy to fill the gaps is to diversify the approaches taken in the enhancement of screening collections. Possible strategies include investments through proven methods, exploring areas of chemical space previously neglected (e.g. hydrophilic compounds, natural product mimics), and applying tactics to the lead discovery process that are complementary to HTS (e.g. fragment based screening or multidisciplinary team efforts to tackle new target classes).
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Affiliation(s)
- David H Drewry
- Molecular Discovery Research, GlaxoSmithKline, 5 Moore Drive, Research Triangle Park, NC 27709, USA.
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31
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Wang K, Kim D, Dömling A. Cyanoacetamide MCR (III): three-component Gewald reactions revisited. JOURNAL OF COMBINATORIAL CHEMISTRY 2010; 12:111-8. [PMID: 19958011 PMCID: PMC3721980 DOI: 10.1021/cc9001586] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanoacetic acid derivatives are the starting materials for a plethora of multicomponent reaction (MCR) scaffolds. Here we describe valuable general protocols for the synthesis of arrays of 2-aminothiophene-3-carboxamides from cyanoacetamides, aldehydes or ketones, and sulfur via a Gewald-3CR variation. In many cases the reactions involve a very convenient work up by simple precipitation in water and filtration. More than 40 new products are described. We foresee our protocol and the resulting derivatives to become very valuable to greatly expanding the MCR scaffold space of cyanoacetamide derivatives.
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Affiliation(s)
- Kan Wang
- University of Pittsburgh, Drug Discovery Institute, Pittsburgh 15261, USA
| | - Dabin Kim
- University of Pittsburgh, Drug Discovery Institute, Pittsburgh 15261, USA
| | - Alexander Dömling
- University of Pittsburgh, Drug Discovery Institute, Pittsburgh 15261, USA
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