1
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Caramiello A, Bellucci MC, Marti-Rujas J, Sacchetti A, Volonterio A. Turn-Mimic Hydantoin-Based Loops Constructed by a Sequential Multicomponent Reaction. J Org Chem 2023; 88:15790-15804. [PMID: 37932902 PMCID: PMC10661056 DOI: 10.1021/acs.joc.3c01861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/08/2023]
Abstract
A collection of peptidomimetics characterized by having an aspartic acid motif embedded in a rigid hydantoin heterocycle are synthesized through a sequential multicomponent domino process followed by standard regioselective deprotection/coupling reactions based on acid-base liquid/liquid purification protocols. 1H nuclear magnetic resonance experiments, molecular modeling, and X-ray analysis showed that the resulting hydantoin-based loops I (in particular) and II (to a lesser extent) can be considered novel β-turn inducer motifs being able to project two peptide-like strands in a U-shaped conformation driven by the formation of intermolecular hydrogen bonds.
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Affiliation(s)
- Alessio
Maria Caramiello
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, Milano 20133, Italy
| | - Javier Marti-Rujas
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Material and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, Milano 20131, Italy
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2
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Caramiello A, Bellucci MC, Cristina G, Castellano C, Meneghetti F, Mori M, Secundo F, Viani F, Sacchetti A, Volonterio A. Synthesis and Conformational Analysis of Hydantoin-Based Universal Peptidomimetics. J Org Chem 2023; 88:10381-10402. [PMID: 36226862 PMCID: PMC10407853 DOI: 10.1021/acs.joc.2c01903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Indexed: 11/30/2022]
Abstract
The synthesis of a collection of enantiomerically pure, systematically substituted hydantoins as structural privileged universal mimetic scaffolds is presented. It relies on a chemoselective condensation/cyclization domino process between isocyanates of quaternary or unsubstituted α-amino esters and N-alkyl aspartic acid diesters followed by standard hydrolysis/coupling reactions with amines, using liquid-liquid acid/base extraction protocols for the purification of the intermediates. Besides the nature of the α carbon on the isocyanate moiety, either a quaternary carbon or a more flexible methylene group, conformational studies in silico (molecular modeling), in solution (NMR, circular dichroism (CD), Fourier transform infrared (FTIR)), and in solid state (X-ray) showed that the presented hydantoin-based peptidomimetics are able to project their substituents in positions superimposable to the side chains of common protein secondary structures such as α-helix and β-turn, being the open α-helix conformation slightly favorable according to molecular modeling, while the closed β-turn conformation preferred in solution and in solid state.
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Affiliation(s)
- Alessio
M. Caramiello
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Maria Cristina Bellucci
- Department
of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133Milano, Italy
| | - Gaetano Cristina
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Carlo Castellano
- Department
of Chemistry, Università degli Studi
di Milano, via Golgi
19, 20133Milano, Italy
| | - Fiorella Meneghetti
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Matteo Mori
- Department
of Pharmaceutical Sciences, Università
degli Studi di Milano, via Mangiagalli 25, 20133Milano, Italy
| | - Francesco Secundo
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Fiorenza Viani
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
| | - Alessandro Sacchetti
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
| | - Alessandro Volonterio
- Department
of Chemistry, Materials and Chemical Engineering “Giulio Natta”, Politecnico di Milano, via Mancinelli 7, 20131Milano, Italy
- Consiglio
Nazionale delle Ricerche, Istituto di Scienze
e Tecnologie Chimiche “G. Natta” (SCITEC), via Mario Bianco 9, 20131Milan, Italy
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3
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Kumar V. Designed Synthesis of Diversely Substituted Hydantoins and Hydantoin-Based Hybrid Molecules: A Personal Account. Synlett 2021. [DOI: 10.1055/a-1480-6474] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractHydantoin and its analogues such as thiohydantoin and iminohydantoin have received substantial attention from both a chemical and a biological point of view. Several compounds of this class have shown useful pharmacological activities such as anticonvulsant, antitumor, antiarrhythmic, and herbicidal properties that have led, in some cases, to clinical applications. Because of these broad-spectrum activities, intensive research efforts have been dedicated in industry and academia to the synthesis and structural modifications of hydantoin and its derivatives. Realizing the importance of hydantoin in organic and medicinal chemistry, we also initiated a research program that successfully designed and developed new routes and methods for the formation of hydantoin, thiohydantoin, and iminohydantoin substituted at various positions, particularly at the N-1 position without following a protection–deprotection strategy. Because combinations of two or more pharmacophoric groups can lead to hybrid molecules that display a mixed mechanism of action on biological targets, we extended our developed strategy to the syntheses of new types of hydantoin-based hybrid molecules by combining hydantoin with a triazole, isoxazoline, or phosphate scaffold as a second pharmacophore to exploit their diverse biological functions.1 Introduction2 Chemistry and Properties2.1 Physical Properties2.2 Chemical Properties2.3 Biological Properties3 General Synthetic Methods4 Synthesis of Diversely Substituted Hydantoins5 Synthesis of Diversely Substituted Thiohydantoins6 Synthesis of Diversely Substituted Iminohydantoins7 Fused or Bicyclic (Thio)hydantoins8 Di- or Multivalent (Thio)hydantoins9 Hydantoin-Based Hybrid Molecules9.1 Hydantoin–Isooxazoline Hybrids9.2 Hydantoin–Triazole Hybrids9.3 Hydantoin–Phosphate Hybrids: Phosphorylated Hydantoins10 Summary and Outlook
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4
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Hegedüs Z, Hóbor F, Shoemark DK, Celis S, Lian LY, Trinh CH, Sessions RB, Edwards TA, Wilson AJ. Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation. Chem Sci 2021; 12:2286-2293. [PMID: 34163995 PMCID: PMC8179271 DOI: 10.1039/d0sc05694d] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 12/01/2020] [Indexed: 12/26/2022] Open
Abstract
β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.
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Affiliation(s)
- Zsófia Hegedüs
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Fruzsina Hóbor
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Deborah K Shoemark
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Sergio Celis
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Lu-Yun Lian
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool Liverpool L69 3BX UK
| | - Chi H Trinh
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Richard B Sessions
- School of Biochemistry, Biomedical Sciences Building, University of Bristol Bristol BS8 1TD UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- School of Molecular and Cellular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology, University of Leeds Woodhouse Lane Leeds LS2 9JT UK
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5
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Vallade M, Jewginski M, Fischer L, Buratto J, Bathany K, Schmitter JM, Stupfel M, Godde F, Mackereth CD, Huc I. Assessing Interactions between Helical Aromatic Oligoamide Foldamers and Protein Surfaces: A Tethering Approach. Bioconjug Chem 2019; 30:54-62. [PMID: 30395443 DOI: 10.1021/acs.bioconjchem.8b00710] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Helically folded aromatic foldamers may constitute suitable candidates for the ab initio design of ligands for protein surfaces. As preliminary steps toward the exploration of this hypothesis, a tethering approach was developed to detect interactions between a protein and a foldamer by confining the former at the surface of the latter. Cysteine mutants of two therapeutically relevant enzymes, CypA and IL4, were produced. Two series of ten foldamers were synthesized bearing different proteinogenic side chains and either a long or a short linker functionalized with an activated disulfide. Disulfide exchange between the mutated cysteines and the activated disulfides yielded 20 foldamer-IL4 and 20 foldamer-CypA adducts. Effectiveness of the reaction was demonstrated by LC-MS, by MS analysis after proteolytic digestion, and by 2D NMR. Circular dichroism then revealed diastereoselective interactions between the proteins and the foldamers confined at their surface which resulted in a preferred handedness of the foldamer helix. Helix sense bias occurred sometimes with both the short and the long linkers and sometimes with only one of them. In a few cases, helix handedness preference is found to be close to quantitative. These cases constitute valid candidates for structural elucidation of the interactions involved.
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Affiliation(s)
- Maëlle Vallade
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Michal Jewginski
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France.,Department of Bioorganic Chemistry, Faculty of Chemistry , Wrocław University of Technology , 50-370 Wrocław , Poland
| | - Lucile Fischer
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Jérémie Buratto
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Katell Bathany
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Jean-Marie Schmitter
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Marine Stupfel
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Frédéric Godde
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Cameron D Mackereth
- Université Bordeaux, INSERM, CNRS, ARNA (U 1212 and UMR 5320), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France
| | - Ivan Huc
- Université Bordeaux, CNRS, IPB, CBMN (UMR 5248), Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33600 Pessac , France.,Department Pharmazie , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 München , Germany
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6
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Kim JK, Lim HJ, Jeong KC, Park SJ. One-pot sequential synthesis of tetrasubstituted thiophenes via sulfur ylide-like intermediates. Beilstein J Org Chem 2018; 14:243-252. [PMID: 29441144 PMCID: PMC5789428 DOI: 10.3762/bjoc.14.16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 01/10/2018] [Indexed: 11/23/2022] Open
Abstract
Herein, we describe a novel approach for the practical synthesis of tetrasubstituted thiophenes 8. The developed method was particularly used for the facile preparation of thienyl heterocycles 8. The mechanism for this reaction is based on the formation of a sulfur ylide-like intermediate. It was clearly suggested by (i) the intramolecular cyclization of ketene N,S-acetals 7 to the corresponding thiophenes 8, (ii) 1H NMR studies of Meldrum's acid-substituted aminothioacetals 9, and (iii) substitution studies of the methoxy group on Meldrum's acid containing N,S-acetals 9b. Notably, in terms of structural effects on the reactivity and stability of sulfur ylide-like intermediates, 2-pyridyl substituted compound 7a exhibited superior properties over those of others.
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Affiliation(s)
- Jun Ki Kim
- Research Center for Medicinal Chemistry, Korea Research Institute of Chemical Technology (KRICT), 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea
- Department of Chemistry, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea
| | - Hwan Jung Lim
- Research Center for Medicinal Chemistry, Korea Research Institute of Chemical Technology (KRICT), 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea
| | - Kyung Chae Jeong
- Translational Research Branch, National Cancer Center, 323 Ilsan-ro, Ilsandong-gu, Goyang-si Gyeonggi-do 10408, Korea
| | - Seong Jun Park
- Research Center for Medicinal Chemistry, Korea Research Institute of Chemical Technology (KRICT), 141 Gajeong-ro, Yuseong-gu, Daejeon 34114, Korea
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7
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Bellucci MC, Frigerio M, Castellano C, Meneghetti F, Sacchetti A, Volonterio A. Design, synthesis, and conformational analysis of 3-cyclo-butylcarbamoyl hydantoins as novel hydrogen bond driven universal peptidomimetics. Org Biomol Chem 2018; 16:521-525. [PMID: 29210413 DOI: 10.1039/c7ob02680c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A collection of systematically substituted 3-cyclo-butylcarbamoyl hydantoins was synthesized by a regioselective multicomponent domino process followed by easy coupling reactions. Calculations, NMR studies and X-ray analysis show that these scaffolds are able to project their side chains similar to common secondary structures, such as the α-helix and β-turn, with favourable enthalpic and entropic profiles.
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Affiliation(s)
- M C Bellucci
- Department of Food, Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
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8
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Konnert L, Lamaty F, Martinez J, Colacino E. Recent Advances in the Synthesis of Hydantoins: The State of the Art of a Valuable Scaffold. Chem Rev 2017. [PMID: 28644621 DOI: 10.1021/acs.chemrev.7b00067] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The review highlights the hydantoin syntheses presented from the point of view of the preparation methods. Novel synthetic routes to various hydantoin structures, the advances brought to the classical methods in the aim of producing more sustainable and environmentally friendly procedures for the preparation of these biomolecules, and a critical comparison of the different synthetic approaches developed in the last twelve years are also described. The review is composed of 95 schemes, 8 figures and 528 references for the last 12 years and includes the description of the hydantoin-based marketed drugs and clinical candidates.
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Affiliation(s)
- Laure Konnert
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Frédéric Lamaty
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Jean Martinez
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Evelina Colacino
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
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9
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Abstract
Bio-inspired synthetic backbones leading to foldamers can provide effective biopolymer mimics with new and improved properties in a physiological environment, and in turn could serve as useful tools to study biology and lead to practical applications in the areas of diagnostics or therapeutics. Remarkable progress has been accomplished over the past 20 years with the discovery of many potent bioactive foldamers originating from diverse backbones and targeting a whole spectrum of bio(macro)molecules such as membranes, protein surfaces, and nucleic acids. These current achievements, future opportunities, and key challenges that remain are discussed in this article.
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10
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Jouanne M, Voisin-Chiret AS, Legay R, Coufourier S, Rault S, Sopkova-de Oliveira Santos J. β-Strand Mimicry: Exploring Oligothienylpyridine Foldamers. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600882] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Marie Jouanne
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
| | - Anne Sophie Voisin-Chiret
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
| | - Rémi Legay
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
| | - Sébastien Coufourier
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
| | - Sylvain Rault
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
| | - Jana Sopkova-de Oliveira Santos
- Université Caen Normandie; Caen France
- UNICAEN; CERMN - EA 4258; FR CNRS 3038 INC3M, SF 4206 ICORE; bd Becquerel 14032 Caen France
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11
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Stucchi M, Grazioso G, Lammi C, Manara S, Zanoni C, Arnoldi A, Lesma G, Silvani A. Disrupting the PCSK9/LDLR protein–protein interaction by an imidazole-based minimalist peptidomimetic. Org Biomol Chem 2016; 14:9736-9740. [DOI: 10.1039/c6ob01642a] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report on a tetraimidazole-based β-strand minimalist peptidomimetic as a novel inhibitor of LDLR–PCSK9 protein–protein interaction, a promising target for hypercholesterolemia.
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Affiliation(s)
- Mattia Stucchi
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
- Dipartimento di Scienze della Vita
| | - Giovanni Grazioso
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Carmen Lammi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Silvia Manara
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Chiara Zanoni
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Anna Arnoldi
- Dipartimento di Scienze Farmaceutiche
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Giordano Lesma
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
| | - Alessandra Silvani
- Dipartimento di Chimica
- Università degli Studi di Milano
- 20133 Milano
- Italy
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12
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Yamashita T, Knipe PC, Busschaert N, Thompson S, Hamilton AD. A Modular Synthesis of Conformationally Preorganised Extended β-Strand Peptidomimetics. Chemistry 2015; 21:14699-702. [DOI: 10.1002/chem.201501366] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Indexed: 12/28/2022]
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13
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German EA, Ross JE, Knipe PC, Don MF, Thompson S, Hamilton AD. β-Strand mimetic foldamers rigidified through dipolar repulsion. Angew Chem Int Ed Engl 2015; 54:2649-52. [PMID: 25599889 DOI: 10.1002/anie.201410290] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/24/2022]
Abstract
Many therapeutically relevant protein-protein interactions contain hot-spot regions on secondary structural elements, which contribute disproportionately to binding enthalpy. Mimicry of such α-helical regions has met with considerable success, however the analogous approach for the β-strand has received less attention. Presented herein is a foldamer for strand mimicry in which dipolar repulsion is a central determinant of conformation. Computation as well as solution- and solid-phase data are consistent with an ensemble weighted almost exclusively in favor of the desired conformation.
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Affiliation(s)
- Elizabeth A German
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) http://hamilton.chem.ox.ac.uk
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14
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German EA, Ross JE, Knipe PC, Don MF, Thompson S, Hamilton AD. β-Strand Mimetic Foldamers Rigidified through Dipolar Repulsion. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410290] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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15
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Zhang YC, Zhang DW, Wang H, Zhou Y, Li ZT. Bipyridinium radical cation dimerization-driven polymeric pleated foldamers and a homoduplex that undergo ion-tuned interconversion. Polym Chem 2015. [DOI: 10.1039/c5py00419e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Radical cation dimerization induces bipyridinium-derived polymers to form pleated secondary structures and a homoduplex which can be tuned by ammonium to interconvert.
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Affiliation(s)
- Yun-Chang Zhang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Dan-Wei Zhang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Hui Wang
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Yaming Zhou
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
| | - Zhan-Ting Li
- Department of Chemistry
- Collaborative Innovation Center of Chemistry for Energy Materials (iChEM)
- Fudan University
- Shanghai 200433
- China
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16
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Robinson CW, Rye CS, Chessum NEA, Jones K. A model β-sheet interaction and thermodynamic analysis of β-strand mimetics. Org Biomol Chem 2015; 13:7402-7. [DOI: 10.1039/c5ob00886g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Two novel β-strand mimetics are synthesized and their binding to a model peptide is studied in detail by 1H NMR.
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Affiliation(s)
- Colin W. Robinson
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Carl S. Rye
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Nicola E. A. Chessum
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
| | - Keith Jones
- Cancer Research UK Cancer Therapeutics Unit
- Institute of Cancer Research
- Haddow Laboratories
- London
- UK
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17
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18
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Powell NH, Clarkson GJ, Notman R, Raubo P, Martin NG, Shipman M. Synthesis and structure of oxetane containing tripeptide motifs. Chem Commun (Camb) 2014; 50:8797-800. [PMID: 24968282 DOI: 10.1039/c4cc03507k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A new class of peptidomimetic is reported in which one of the amide C=O bonds of the peptide backbone is replaced by an oxetane ring. They are synthesised by conjugate addition of various α-amino esters to a 3-(nitromethylene)oxetane, reduction of the nitro group and further coupling with N-Z protected amino acids to grow the peptide chain. Structural insights are provided by X-ray diffraction and molecular dynamics simulations.
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Affiliation(s)
- Nicola H Powell
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK.
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19
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20
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Chua KCH, Pietsch M, Zhang X, Hautmann S, Chan HY, Bruning JB, Gütschow M, Abell AD. Macrocyclic Protease Inhibitors with Reduced Peptide Character. Angew Chem Int Ed Engl 2014; 53:7828-31. [DOI: 10.1002/anie.201404301] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Indexed: 01/14/2023]
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21
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Singleton ML, Castellucci N, Massip S, Kauffmann B, Ferrand Y, Huc I. Synthesis of 1,8-diazaanthracenes as building blocks for internally functionalized aromatic oligoamide foldamers. J Org Chem 2014; 79:2115-22. [PMID: 24506270 DOI: 10.1021/jo402852m] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The synthesis of a variety of 9-functionalized 1,8-diazaanthracene diesters and amino acids is described. Derivatization at the 9-position relies on facile reactions performed on the 9-chloro and 9-bromomethyl precursors. This has allowed the incorporation of nucleophilic or sensitive functional groups that otherwise cannot be incorporated under standard methods for synthesizing these compounds. Additionally, the synthesis of the protected amino acids via a high-yielding monosaponification and subsequent Curtius rearrangement has been accomplished on a multigram scale. These units, together with the functionalized derivatives, should prove to be useful monomers in the synthesis of aromatic oligoamide foldamers.
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Affiliation(s)
- Michael L Singleton
- University of Bordeaux, CBMN (UMR 5248), Institut Européen de Chimie Biologie, 2 rue Robert Escarpit, 33600 Pessac, France
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22
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Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Diphenylacetylene-linked peptide strands induce bidirectional β-sheet formation. Angew Chem Int Ed Engl 2014; 53:3650-3. [PMID: 24554626 DOI: 10.1002/anie.201309353] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2013] [Revised: 12/17/2013] [Indexed: 12/31/2022]
Abstract
In the search for synthetic mimics of protein secondary structures relevant to the mediation of protein-protein interactions, we have synthesized a series of tetrasubstituted diphenylacetylenes that display β-sheet structures in two directions. Extensive X-ray crystallographic and NMR solution phase studies are consistent with these proteomimetics adopting sheet structures, displaying both hydrophobic and hydrophilic amino acid side chains.
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Affiliation(s)
- Hannah Lingard
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) http://hamilton.chem.ox.ac.uk
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23
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Lingard H, Han JT, Thompson AL, Leung IKH, Scott RTW, Thompson S, Hamilton AD. Diphenylacetylene-Linked Peptide Strands Induce Bidirectional β-Sheet Formation. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201309353] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Nevola L, Rodriguez JM, Thompson S, Hamilton AD. Super-secondary structure peptidomimetics: design and synthesis of an α-α hairpin analogue. Supramol Chem 2013; 25:586-590. [PMID: 26052191 DOI: 10.1080/10610278.2013.817581] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The α-α helix motif presents key recognition domains in protein-protein and protein-oligonucleotide binding, and is one of the most common super-secondary structures. Herein we describe the design, synthesis and structural characterization of an α-α hairpin analogue based on a tetra-coordinated Pd(II) bis-(iminoisoquinoline) complex as a template for the display of two α-helix mimics. This approach is exemplified by the attachment of two biphenyl peptidomimetics to reproduce the side-chains of the i and i+4 residues of two helices.
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Affiliation(s)
- Laura Nevola
- Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
| | - Johanna M Rodriguez
- Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
| | - Sam Thompson
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, England
| | - Andrew D Hamilton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, England ; Yale University, Department of Chemistry, P.O. Box 208107, New Haven, CT 06511
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25
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Cruz-Migoni A, Fuentes-Fernandez N, Rabbitts TH. Peptides: minimal drug surrogates to interrogate and interfere with protein function. MEDCHEMCOMM 2013. [DOI: 10.1039/c3md00142c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The interactome in normal and disease cells is a key area for study and therapeutic targeting, yet few molecules have been developed that can interfere with protein–protein interactions within cells. Peptides and homologues are potential reagents to target PPI.
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Affiliation(s)
- A. Cruz-Migoni
- Weatherall Institute of Molecular Medicine
- MRC Molecular Haematology Unit
- University of Oxford
- John Radcliffe Hospital
- Oxford
| | - N. Fuentes-Fernandez
- Institute of Biological, Environmental and Rural Science
- Aberystwyth University
- Aberystwyth
- UK
| | - T. H. Rabbitts
- Weatherall Institute of Molecular Medicine
- MRC Molecular Haematology Unit
- University of Oxford
- John Radcliffe Hospital
- Oxford
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26
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Kang CW, Sun Y, Del Valle JR. Substituted imidazo[1,2-a]pyridines as β-strand peptidomimetics. Org Lett 2012; 14:6162-5. [PMID: 23210770 DOI: 10.1021/ol302850n] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
New conformationally extended dipeptide surrogates based on an imidazo[1,2-a]pyridine scaffold are described. Efficient synthesis and incorporation into host peptides affords structures with native side-chain functionality and hydrogen bonding elements on one face of the backbone. Structural analysis by NMR suggests that model peptidomimetics adopt a β-strand-like conformation in solution.
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Affiliation(s)
- Chang Won Kang
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, United States
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27
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Ngo TH, Berndt H, Lentz D, Reissig HU. Linear and Cyclic Amides with a Thiophene Backbone: Ultrasound-Promoted Synthesis and Crystal Structures. J Org Chem 2012; 77:9676-83. [DOI: 10.1021/jo3017605] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Thien H. Ngo
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195
Berlin, Germany
| | - Hülya Berndt
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195
Berlin, Germany
| | - Dieter Lentz
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195
Berlin, Germany
| | - Hans-Ulrich Reissig
- Institut
für Chemie und Biochemie, Freie Universität Berlin, Takustrasse 3, D-14195
Berlin, Germany
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28
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Haridas V, Sadanandan S, Hundal G, Suresh CH. 1,3-Phenyl linked urea-based receptors for anions and the facile cyclization to imidazolidinedione. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.08.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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29
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Dhara K, Midya GC, Dash J. A Diversity-Oriented Approach to Spirocyclic and Fused Hydantoins via Olefin Metathesis. J Org Chem 2012; 77:8071-82. [DOI: 10.1021/jo301234r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Kalyan Dhara
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
| | - Ganesh Chandra Midya
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata-700032, India
| | - Jyotirmayee Dash
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, West
Bengal 741252, India
- Department
of Organic Chemistry, Indian Association for the Cultivation of Science,
Jadavpur, Kolkata-700032, India
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30
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Sutherell CL, Thompson S, Scott RTW, Hamilton AD. Aryl-linked imidazolidin-2-ones as non-peptidic β-strand mimetics. Chem Commun (Camb) 2012; 48:9834-6. [DOI: 10.1039/c2cc34791a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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31
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