1
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Dengler S, Howard RT, Morozov V, Tsiamantas C, Huang WE, Liu Z, Dobrzanski C, Pophristic V, Brameyer S, Douat C, Suga H, Huc I. Display Selection of a Hybrid Foldamer-Peptide Macrocycle. Angew Chem Int Ed Engl 2023; 62:e202308408. [PMID: 37707879 DOI: 10.1002/anie.202308408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/15/2023]
Abstract
Expanding the chemical diversity of peptide macrocycle libraries for display selection is desirable to improve their potential to bind biomolecular targets. We now have implemented a considerable expansion through a large aromatic helical foldamer inclusion. A foldamer was first identified that undergoes flexizyme-mediated tRNA acylation and that is capable of initiating ribosomal translation with yields sufficiently high to perform an mRNA display selection of macrocyclic foldamer-peptide hybrids. A hybrid macrocyclic nanomolar binder to the C-lobe of the E6AP HECT domain was selected that showed a highly converged peptide sequence. A crystal structure and molecular dynamics simulations revealed that both the peptide and foldamer are helical in an intriguing reciprocal stapling fashion. The strong residue convergence could be rationalized based on their involvement in specific interactions with the target protein. The foldamer stabilizes the peptide helix through stapling and through contacts with key residues. These results altogether represent a significant extension of the chemical space amenable to display selection and highlight possible benefits of inserting an aromatic foldamer into a peptide macrocycle for the purpose of protein recognition.
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Affiliation(s)
- Sebastian Dengler
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Ryan T Howard
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Vasily Morozov
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Christos Tsiamantas
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Wei-En Huang
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Zhiwei Liu
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Christopher Dobrzanski
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Vojislava Pophristic
- Department of Chemistry & Biochemistry, Rowan University, 201 Mullica Hill Road, 08028, Glassboro, New Jersey, USA
| | - Sophie Brameyer
- Biozentrum, Microbiology, Ludwig-Maximilians-Universität, Großhaderner Str. 2-4, 82152, Martinsried, Germany
| | - Céline Douat
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
| | - Hiroaki Suga
- Department of Chemistry, School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo, 113-0033, Tokyo, Japan
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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2
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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3
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Jang HJ, Lee S, An BJ, Song G, Jeon HG, Jeong KS. Tweezer-type binding cavity formed by the helical folding of a carbazole-pyridine oligomer. Chem Commun (Camb) 2022; 58:1410-1413. [PMID: 34994755 DOI: 10.1039/d1cc06569f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have synthesised a new aromatic foldamer based on the carbazole-pyridine oligomers that adopt helical conformations via dipole-dipole interactions and π-stacking between two ethynyl bond-linked monomers. This foldamer scaffold has been further modified into a synthetic receptor with a tweezer-type binding cavity outside the helical backbone upon folding, in contrast to most aromatic foldamers with internal binding cavities. The tweezer-type cavity is composed of two parallel pyrenyl planes, allowing for the intercalation of a naphthalenediimide guest via π-stacking and CH⋯O interactions, as demonstrated using its 1H NMR spectra and X-ray crystal structure.
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Affiliation(s)
- Hye Jin Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Seungwon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Byung Jun An
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Geunmoo Song
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Hae-Geun Jeon
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
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4
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Biagiotti G, Angeli A, Giacomini A, Toniolo G, Landini L, Salerno G, Di Cesare Mannelli L, Ghelardini C, Mello T, Mussi S, Ravelli C, Marelli M, Cicchi S, Menna E, Ronca R, Supuran CT, Richichi B. Glyco-Coated CdSe/ZnS Quantum Dots as Nanoprobes for Carbonic Anhydrase IX Imaging in Cancer Cells. ACS APPLIED NANO MATERIALS 2021; 4:14153-14160. [PMID: 34970641 PMCID: PMC8713163 DOI: 10.1021/acsanm.1c03603] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The bioimaging of cancer cells by the specific targeting of overexpressed biomarkers is an approach that holds great promise in the identification of selective diagnostic tools. Tumor-associated human carbonic anhydrase (hCA) isoforms IX and XII have been considered so far as well-defined biomarkers, with their expression correlating with cancer progression and aggressiveness. Therefore, the availability of highly performant fluorescent tools tailored for their targeting and able to efficiently visualize such key targets is in high demand. We report here on the design and synthesis of a kind of quantum dot (QD)-based fluorescent glyconanoprobe coated with a binary mixture of ligands, which, according to the structure of the terminal domains, impart specific property sets to the fluorescent probe. Specifically, monosaccharide residues ensured the dispersibility in the biological medium, CA inhibitor residues provided specific targeting of membrane-anchored hCA IX overexpressed on bladder cancer cells, and the quantum dots imparted the optical/fluorescence properties.
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Affiliation(s)
- Giacomo Biagiotti
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM, Via G. Giusti, 9, 50121 Firenze, Florence, Italy
| | - Andrea Angeli
- Department
of Neuroscience, Psychology, Drug Research and Child Health −
NEUROFARBA, Section of Pharmaceutical Chemistry, University of Firenze, Via Ugo Schiff 7, Sesto Fiorentino, 50019 Florence, Italy
| | - Arianna Giacomini
- Department
of Molecular and translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Gianluca Toniolo
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM, Via G. Giusti, 9, 50121 Firenze, Florence, Italy
| | - Luca Landini
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
| | - Gianluca Salerno
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
| | - Lorenzo Di Cesare Mannelli
- Department
of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA
- Pharmacology and Toxicology Section, University
of Firenze, V.le Pieraccini
6, 50139 Firenze, Florence, Italy
| | - Carla Ghelardini
- Department
of Neuroscience, Psychology, Drug Research and Child Health - NEUROFARBA
- Pharmacology and Toxicology Section, University
of Firenze, V.le Pieraccini
6, 50139 Firenze, Florence, Italy
| | - Tommaso Mello
- Department
of Clinical and Experimental Biomedical Sciences “Mario Serio”—Gastroenterology
Unit, University of Firenze, V.le Pieraccini 6, 50139 Firenze, Florence, Italy
| | - Silvia Mussi
- Department
of Molecular and translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Cosetta Ravelli
- Department
of Molecular and translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Marcello Marelli
- Istituto
di scienze e tecnologie chimiche “Giulio Natta”, CNR-SCITEC, Sede Fantoli, Via Fantoli 16/15, 20138 Milano Italy
| | - Stefano Cicchi
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM, Via G. Giusti, 9, 50121 Firenze, Florence, Italy
| | - Enzo Menna
- Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM, Via G. Giusti, 9, 50121 Firenze, Florence, Italy
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy
- Centre
for Mechanics of Biological Materials—CMBM, Via Marzolo 9, 35131 Padova, Italy
| | - Roberto Ronca
- Department
of Molecular and translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Claudiu T. Supuran
- Department
of Neuroscience, Psychology, Drug Research and Child Health −
NEUROFARBA, Section of Pharmaceutical Chemistry, University of Firenze, Via Ugo Schiff 7, Sesto Fiorentino, 50019 Florence, Italy
| | - Barbara Richichi
- Department
of Chemistry “Ugo Schiff”, University of Firenze, Via della Lastruccia 13, Sesto Fiorentino, 50019 Florence, Italy
- Consorzio
Interuniversitario Nazionale per la Scienza e Tecnologia dei Materiali (INSTM, Via G. Giusti, 9, 50121 Firenze, Florence, Italy
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5
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Bindl D, Heinemann E, Mandal PK, Huc I. Quantitative helix handedness bias through a single H vs. CH 3 stereochemical differentiation. Chem Commun (Camb) 2021; 57:5662-5665. [PMID: 33972976 DOI: 10.1039/d1cc01452h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
A novel chiral aromatic δ-amino acid building block was shown to fully induce handedness in quinoline oligoamide foldamers with the possibility of further increasing the bias by combining multiples of these units in the same sequence. Through its incorporation within the helix, both N- and C-termini are still accessible for further functionalisation.
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Affiliation(s)
- Daniel Bindl
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, München 81377, Germany.
| | - Elisabeth Heinemann
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, München 81377, Germany.
| | - Pradeep K Mandal
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, München 81377, Germany.
| | - Ivan Huc
- Department of Pharmacy and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstraße 5-13, München 81377, Germany.
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6
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Zheng L, Guo S, Wang C, Wang Y, Fan Y, Chen X, Zhang K, Jiang H. Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains. Chempluschem 2021; 86:340-346. [PMID: 33624952 DOI: 10.1002/cplu.202000824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/13/2021] [Indexed: 11/09/2022]
Abstract
A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by 1 H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.
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Affiliation(s)
- Lu Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, P. R. China
| | - Shengzhu Guo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Chu Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanqing Fan
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Hua Jiang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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7
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Reddy PS, Langlois d'Estaintot B, Granier T, Mackereth CD, Fischer L, Huc I. Structure Elucidation of Helical Aromatic Foldamer-Protein Complexes with Large Contact Surface Areas. Chemistry 2019; 25:11042-11047. [PMID: 31257622 DOI: 10.1002/chem.201902942] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Indexed: 01/12/2023]
Abstract
The development of large synthetic ligands could be useful to target the sizeable surface areas involved in protein-protein interactions. Herein, we present long helical aromatic oligoamide foldamers bearing proteinogenic side chains that cover up to 450 Å2 of the human carbonic anhydrase II (HCA) surface. The foldamers are composed of aminoquinolinecarboxylic acids bearing proteinogenic side chains and of more flexible aminomethyl-pyridinecarboxylic acids that enhance helix handedness dynamics. Crystal structures of HCA-foldamer complexes were obtained with a 9- and a 14-mer both showing extensive protein-foldamer hydrophobic contacts. In addition, foldamer-foldamer interactions seem to be prevalent in the crystal packing, leading to the peculiar formation of an HCA superhelix wound around a rod of stacked foldamers. Solution studies confirm the positioning of the foldamer at the protein surface as well as a dimerization of the complexes.
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Affiliation(s)
- Post Sai Reddy
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Béatrice Langlois d'Estaintot
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Thierry Granier
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Cameron D Mackereth
- ARNA (U1212), Univ. Bordeaux-INSERM-CNRS, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Lucile Fischer
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France
| | - Ivan Huc
- CBMN (UMR5248), Univ. Bordeaux-CNRS-INP, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600, Pessac, France.,Department Pharmazie and Center for Integrated Protein Science, Ludwig-Maximilians-Universität, Butenandtstr. 5-13, 81377, München, Germany
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8
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Alex JM, Corvaglia V, Hu X, Engilberge S, Huc I, Crowley PB. Crystal structure of a protein–aromatic foldamer composite: macromolecular chiral resolution. Chem Commun (Camb) 2019; 55:11087-11090. [DOI: 10.1039/c9cc05330a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A protein–foldamer crystal structure illustrates protein assembly by a sulfonated aromatic oligoamide, and chiral resolution of the foldamer helix handedness.
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Affiliation(s)
- Jimi M. Alex
- School of Chemistry
- National University of Ireland
- Galway
- Ireland
| | - Valentina Corvaglia
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | - Xiaobo Hu
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
| | | | - Ivan Huc
- Universite de Bordeaux
- CNRS
- Bordeaux Institut National Polytechnique, CBMN (UMR 5248)
- Institut Europeen de Chimie et Biologie
- Pessac 33600
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