1
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Liu D, Yan J, Ma F, Wang J, Yan S, He W. Reinvigoration of cytotoxic T lymphocytes in microsatellite instability-high colon adenocarcinoma through lysosomal degradation of PD-L1. Nat Commun 2024; 15:6922. [PMID: 39134545 PMCID: PMC11319731 DOI: 10.1038/s41467-024-51386-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
Compensation and intracellular storage of PD-L1 may compromise the efficacy of antibody drugs targeting the conformational blockade of PD1/PD-L1 on the cell surface. Alternative therapies aiming to reduce the overall cellular abundance of PD-L1 thus might overcome resistance to conventional immune checkpoint blockade. Here we show by bioinformatics analysis that colon adenocarcinoma (COAD) with high microsatellite instability (MSI-H) presents the most promising potential for this therapeutic intervention, and that overall PD-L1 abundance could be controlled via HSC70-mediated lysosomal degradation. Proteomic and metabolomic analyses of mice COAD with MSI-H in situ unveil a prominent acidic tumor microenvironment. To harness these properties, an artificial protein, IgP β, is engineered using pH-responsive peptidic foldamers. This features customized peptide patterns and designed molecular function to facilitate interaction between neoplastic PD-L1 and HSC70. IgP β effectively reduces neoplastic PD-L1 levels via HSC70-mediated lysosomal degradation, thereby persistently revitalizing the action of tumor-infiltrating CD8 + T cells. Notably, the anti-tumor effect of lysosomal-degradation-based therapy surpasses that of antibody-based immune checkpoint blockade for MSI-H COAD in multiple mouse models. The presented strategy expands the use of peptidic foldamers in discovering artificial protein drugs for targeted cancer immunotherapy.
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Affiliation(s)
- Dan Liu
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Jin Yan
- Department of infectious Diseases, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
- Department of Tumor and Immunology in precision medical institute, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
| | - Fang Ma
- Department of Tumor and Immunology in precision medical institute, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China
| | - Jingmei Wang
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Siqi Yan
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Wangxiao He
- Department of Medical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
- Department of Talent Highland, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, PR China.
- Institute for Stem Cell & Regenerative Medicine, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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2
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Hóbor F, Hegedüs Z, Ibarra AA, Petrovicz VL, Bartlett GJ, Sessions RB, Wilson AJ, Edwards TA. Understanding p300-transcription factor interactions using sequence variation and hybridization. RSC Chem Biol 2022; 3:592-603. [PMID: 35656479 PMCID: PMC9092470 DOI: 10.1039/d2cb00026a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/10/2022] [Indexed: 11/21/2022] Open
Abstract
The hypoxic response is central to cell function and plays a significant role in the growth and survival of solid tumours. HIF-1 regulates the hypoxic response by activating over 100...
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Affiliation(s)
- 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
| | - Zsófia Hegedüs
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Amaurys Avila Ibarra
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Vencel L Petrovicz
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H-6720 Szeged Hungary
| | - Gail J Bartlett
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Richard B Sessions
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TD UK
- BrisSynBio, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane Leeds LS2 9JT UK
- School of Chemistry, University of Leeds Woodhouse Lane Leeds LS2 9JT 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
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3
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Joy ST, Henley MJ, De Salle SN, Beyersdorf MS, Vock IW, Huldin AJL, Mapp AK. A Dual-Site Inhibitor of CBP/p300 KIX is a Selective and Effective Modulator of Myb. J Am Chem Soc 2021; 143:15056-15062. [PMID: 34491719 DOI: 10.1021/jacs.1c04432] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The protein-protein interaction between the KIX motif of the transcriptional coactivator CBP/p300 and the transcriptional activator Myb is a high-value target due to its established role in certain acute myeloid leukemias (AML) and potential contributions to other cancers. However, the CBP/p300 KIX domain has multiple binding sites, several structural homologues, many binding partners, and substantial conformational plasticity, making it challenging to specifically target using small-molecule inhibitors. Here, we report a picomolar dual-site inhibitor (MybLL-tide) of the Myb-CBP/p300 KIX interaction. MybLL-tide has higher affinity for CBP/p300 KIX than any previously reported compounds while also possessing 5600-fold selectivity for the CBP/p300 KIX domain over other coactivator domains. MybLL-tide blocks the association of CBP and p300 with Myb in the context of the proteome, leading to inhibition of key Myb·KIX-dependent genes in AML cells. These results show that MybLL-tide is an effective, modifiable tool to selectively target the KIX domain and assess transcriptional effects in AML cells and potentially other cancers featuring aberrant Myb behavior. Additionally, the dual-site design has applicability to the other challenging coactivators that bear multiple binding surfaces.
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Affiliation(s)
- Stephen T Joy
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Madeleine J Henley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Samantha N De Salle
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Matthew S Beyersdorf
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Isaac W Vock
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Interdisciplinary Research Experiences for Undergraduates Program, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Allison J L Huldin
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anna K Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
- Program in Chemical Biology, University of Michigan, Ann Arbor, Michigan 48109, United States
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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4
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Delfosse P, Seaton CC, Male L, Lord RM, Pike SJ. Influence of Terminal Functionality on the Crystal Packing Behaviour and Cytotoxicity of Aromatic Oligoamides. Front Chem 2021; 9:709161. [PMID: 34277574 PMCID: PMC8277928 DOI: 10.3389/fchem.2021.709161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 06/10/2021] [Indexed: 11/13/2022] Open
Abstract
The synthesis and characterization of three aromatic oligoamides, constructed from the same pyridyl carboxamide core but incorporating distinct end groups of acetyl (Ac) 1, tert-butyloxycarbonyl (Boc) 2 and amine 3 is reported. Single crystal X-ray diffraction analysis of 1-3 and a dimethylsulfoxide (DMSO) solvate of 2 (2-DMSO), has identified the presence of a range of intra- and intermolecular interactions including N-H⋯N, N-H⋯O=C and N-H⋯O=S(CH3)2 hydrogen-bonding interactions, C-H⋯π interactions and off-set, face-to-face stacking π-π interactions that support the variety of slipped stack, herringbone and cofacial crystal packing arrangements observed in 1-3. Additionally, the cytotoxicity of this series of aromatic oligoamides was assessed against two human ovarian (A2780 and A2780cisR), two human breast (MCF-7 and MDA-MB-231) cancerous cell lines and one non-malignant human epithelial cell line (PNT-2), to investigate the influence of the terminal functionality of these aromatic oligoamides on their biological activity. The chemosensitivity results highlight that modification of the terminal group from Ac to Boc in 1 and 2 leads to a 3-fold increase in antiproliferative activity against the cisplatin-sensitive ovarian carcinoma cell line, A2780. The presence of the amine termini in 3 gave the only member of the series to display activity against the cisplatin-resistance ovarian carcinoma cell line, A2780cisR. Compound 2 is the lead candidate of this series, displaying high selectivity towards A2780 cancer cells when compared to non-malignant PNT-2 cells, with a selectivity index value >4.2. Importantly, this compound is more selective towards A2780 (cf. PNT-2) than the clinical platinum drugs oxaliplatin by > 2.6-fold and carboplatin by > 1.6-fold.
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Affiliation(s)
- Pierre Delfosse
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
| | - Colin C. Seaton
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
| | - Louise Male
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
| | - Rianne M. Lord
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
- School of Chemistry, University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Sarah J. Pike
- School of Chemistry and Biosciences, University of Bradford, Bradford, United Kingdom
- School of Chemistry, University of Birmingham, Birmingham, United Kingdom
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5
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Mbianda J, Bakail M, André C, Moal G, Perrin ME, Pinna G, Guerois R, Becher F, Legrand P, Traoré S, Douat C, Guichard G, Ochsenbein F. Optimal anchoring of a foldamer inhibitor of ASF1 histone chaperone through backbone plasticity. SCIENCE ADVANCES 2021; 7:7/12/eabd9153. [PMID: 33741589 PMCID: PMC7978421 DOI: 10.1126/sciadv.abd9153] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/27/2021] [Indexed: 05/08/2023]
Abstract
Sequence-specific oligomers with predictable folding patterns, i.e., foldamers, provide new opportunities to mimic α-helical peptides and design inhibitors of protein-protein interactions. One major hurdle of this strategy is to retain the correct orientation of key side chains involved in protein surface recognition. Here, we show that the structural plasticity of a foldamer backbone may notably contribute to the required spatial adjustment for optimal interaction with the protein surface. By using oligoureas as α helix mimics, we designed a foldamer/peptide hybrid inhibitor of histone chaperone ASF1, a key regulator of chromatin dynamics. The crystal structure of its complex with ASF1 reveals a notable plasticity of the urea backbone, which adapts to the ASF1 surface to maintain the same binding interface. One additional benefit of generating ASF1 ligands with nonpeptide oligourea segments is the resistance to proteolysis in human plasma, which was highly improved compared to the cognate α-helical peptide.
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Affiliation(s)
- Johanne Mbianda
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - May Bakail
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Christophe André
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Gwenaëlle Moal
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Marie E Perrin
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Guillaume Pinna
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Raphaël Guerois
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Francois Becher
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
| | - Pierre Legrand
- Synchrotron SOLEIL, L'Orme des Merisiers, F91190 Gif-sur-Yvette, France
| | - Seydou Traoré
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Céline Douat
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, Institut Européen de Chimie et Biologie, 2 rue Robert Escarpit, F-33607 Pessac, France.
| | - Françoise Ochsenbein
- Institute Joliot, Commissariat à l'énergie Atomique (CEA), Direction de la Recherche Fondamentale (DRF), CEA Saclay, F91191 Gif-sur-Yvette, France.
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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6
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Tököli A, Mag B, Bartus É, Wéber E, Szakonyi G, Simon MA, Czibula Á, Monostori É, Nyitray L, Martinek TA. Proteomimetic surface fragments distinguish targets by function. Chem Sci 2020; 11:10390-10398. [PMID: 34094300 PMCID: PMC8162404 DOI: 10.1039/d0sc03525d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Accepted: 09/09/2020] [Indexed: 11/21/2022] Open
Abstract
The fragment-centric design promises a means to develop complex xenobiotic protein surface mimetics, but it is challenging to find locally biomimetic structures. To address this issue, foldameric local surface mimetic (LSM) libraries were constructed. Protein affinity patterns, ligand promiscuity and protein druggability were evaluated using pull-down data for targets with various interaction tendencies and levels of homology. LSM probes based on H14 helices exhibited sufficient binding affinities for the detection of both orthosteric and non-orthosteric spots, and overall binding tendencies correlated with the magnitude of the target interactome. Binding was driven by two proteinogenic side chains and LSM probes could distinguish structurally similar proteins with different functions, indicating limited promiscuity. Binding patterns displayed similar side chain enrichment values to those for native protein-protein interfaces implying locally biomimetic behavior. These analyses suggest that in a fragment-centric approach foldameric LSMs can serve as useful probes and building blocks for undruggable protein interfaces.
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Affiliation(s)
- Attila Tököli
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Beáta Mag
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Éva Bartus
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Edit Wéber
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
| | - Gerda Szakonyi
- Institute of Pharmaceutical Analysis, University of Szeged Somogyi u. 4. H6720 Szeged Hungary
| | - Márton A Simon
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Ágnes Czibula
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - Éva Monostori
- Lymphocyte Signal Transduction Laboratory, Institute of Genetics, Biological Research Centre Temesvári krt. 62 H6726 Szeged Hungary
| | - László Nyitray
- Department of Biochemistry, Eötvös Loránd University Pázmány Péter sétány 1/C H1077 Budapest Hungary
| | - Tamás A Martinek
- Department of Medical Chemistry, University of Szeged Dóm tér 8 H6720 Szeged Hungary
- MTA-SZTE Biomimetic Systems Research Group, University of Szeged Dóm tér 8 H6720 Szeged Hungary
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7
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Horne WS, Grossmann TN. Proteomimetics as protein-inspired scaffolds with defined tertiary folding patterns. Nat Chem 2020; 12:331-337. [PMID: 32029906 DOI: 10.1038/s41557-020-0420-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Proteins have evolved as a variable platform that provides access to molecules with diverse shapes, sizes and functions. These features have inspired chemists for decades to seek artificial mimetics of proteins with improved or novel properties. Such work has focused primarily on small protein fragments, often isolated secondary structures; however, there has lately been a growing interest in the design of artificial molecules that mimic larger, more complex tertiary folds. In this Perspective, we define these agents as 'proteomimetics' and discuss the recent advances in the field. Proteomimetics can be divided into three categories: protein domains with side-chain functionality that alters the native linear-chain topology; protein domains in which the chemical composition of the polypeptide backbone has been partially altered; and protein-like folded architectures that are composed entirely of non-natural monomer units. We give an overview of these proteomimetic approaches and outline remaining challenges facing the field.
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Affiliation(s)
- W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, the Netherlands.
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8
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Wang X, Zhu G, Liang W, Zhao S, Yuan L, Zhou X, Lu L, Xu H. Design, Synthesis and Docking of Linear and Hairpin‐Like Alpha Helix Mimetics Based on Alkoxylated Oligobenzamide. ChemistrySelect 2019. [DOI: 10.1002/slct.201900171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Xiang Wang
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Guanhua Zhu
- Division of Structural Biology and BiochemistrySchool of Biological SciencesNanyang Technological University
| | - Wenjie Liang
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Siqi Zhao
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Lvbing Yuan
- State Key Laboratory of Structural ChemistryFujian Institute of Research on the Structure of MatterChinese Academy of Sciences
| | - Xiaohu Zhou
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
| | - Lanyuan Lu
- Division of Structural Biology and BiochemistrySchool of Biological SciencesNanyang Technological University
| | - Hai Xu
- College of Chemistry and Chemical EngineeringCentral South University South Lushan Road Changsha, Hunan
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9
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Arrata I, Grison CM, Coubrough HM, Prabhakaran P, Little MA, Tomlinson DC, Webb ME, Wilson AJ. Control of conformation in α-helix mimicking aromatic oligoamide foldamers through interactions between adjacent side-chains. Org Biomol Chem 2019; 17:3861-3867. [PMID: 30938392 DOI: 10.1039/c9ob00123a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design, synthesis and structural characterization of non-natural oligomers that adopt well-defined conformations, so called foldamers, is a key objective in developing biomimetic 3D functional architectures. For the aromatic oligoamide foldamer family, use of interactions between side-chains to control conformation is underexplored. The current manuscript addresses this objective through the design, synthesis and conformational analyses of model dimers derived from 3-O-alkylated para-aminobenzoic acid monomers. The O-alkyl groups on these foldamers are capable of adopting syn- or anti-conformers through rotation around the Ar-CO/NH axes. In the syn-conformation this allows the foldamer to act as a topographical mimic of the α-helix whereby the O-alkyl groups mimic the spatial orientation of the i and i + 4 side-chains from the α-helix. Using molecular modelling and 2D NMR analyses, this work illustrates that covalent links and hydrogen-bonding interactions between side-chains can bias the conformation in favour of the α-helix mimicking syn-conformer, offering insight that may be more widely applied to control secondary structure in foldamers.
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Affiliation(s)
- Irene Arrata
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK.
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10
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Hegedus Z, Grison CM, Miles JA, Rodriguez-Marin S, Warriner SL, Webb ME, Wilson AJ. A catalytic protein-proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S. Chem Sci 2019; 10:3956-3962. [PMID: 31015935 PMCID: PMC6461108 DOI: 10.1039/c9sc00374f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 12/27/2022] Open
Abstract
Foldamers are abiotic molecules that mimic the ability of bio-macromolecules to adopt well-defined and organised secondary, tertiary or quaternary structure. Such templates have enabled the generation of defined architectures which present structurally defined surfaces that can achieve molecular recognition of diverse and complex targets. Far less explored is whether this mimicry of nature can extend to more advanced functions of biological macromolecules such as the generation and activation of catalytic function. In this work, we adopt a novel replacement strategy whereby a segment of protein structure (the S-peptide from RNase S) is replaced by a foldamer that mimics an α-helix. The resultant prosthetic replacement forms a non-covalent complex with the S-protein leading to restoration of catalytic function, despite the absence of a key catalytic residue. Thus this functional protein-proteomimetic complex provides proof that significant segments of protein can be replaced with non-natural building blocks that may, in turn, confer advantageous properties.
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Affiliation(s)
- Zsofia Hegedus
- 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
| | - Claire M Grison
- 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
| | - Jennifer A Miles
- 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
| | - Silvia Rodriguez-Marin
- 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
| | - Stuart L Warriner
- 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
| | - Michael E Webb
- 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
| | - 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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11
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Li J, Xi W, Li X, Sun H, Li Y. Advances in inhibition of protein-protein interactions targeting hypoxia-inducible factor-1 for cancer therapy. Bioorg Med Chem 2019; 27:1145-1158. [PMID: 30819620 DOI: 10.1016/j.bmc.2019.01.042] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/25/2019] [Accepted: 01/31/2019] [Indexed: 12/23/2022]
Abstract
Hypoxia is a common characteristic of many types of solid tumors and is associated with tumor propagation, malignant progression, and resistance to anti-cancer therapy. HIF-1 pathway is one of the survival pathways activated in tumor in response to hypoxia. In hypoxic condition, hypoxia-inducible factor-1α (HIF-1α) is stabilized and translocated into nucleus where it forms heterodimer with HIF-1β and regulates the expression of a plethora of genes involved in different processes, such as cell proliferation, differentiation, apoptosis, vascularization/angiogenesis, tumor invasion and metastasis. Recruitment of co-activator p300 or CBP to HIF-1α is critical to the transactivation activity of HIF-1 dimer, therefore, small molecules which can block the dimerization of HIF-1α and HIF-1β or inhibit the interaction between HIF-1α and p300 can function as inhibitors of HIF-1 and have the potential to be developed as novel therapies for the treatment of human cancers. In this review, recent progress of small molecular inhibitors of protein-protein interactions targeting HIF-1 is summarized, the mechanism of functions of these compounds and their potential usage as anti-cancer agents have also been discussed.
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Affiliation(s)
- Jia Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Wanlin Xi
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Xiaofang Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
| | - Yuyan Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China.
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Arrata I, Barnard A, Tomlinson DC, Wilson AJ. Interfacing native and non-native peptides: using Affimers to recognise α-helix mimicking foldamers. Chem Commun (Camb) 2018; 53:2834-2837. [PMID: 28217789 DOI: 10.1039/c6cc09395g] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Selection methods are used to identify Affimers that recognise α-helix mimicking N-alkylated aromatic oligoamides thus demonstrating foldamer and natural α-amino acid codes are compatible.
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Affiliation(s)
- Irene Arrata
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Anna Barnard
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Darren C Tomlinson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK. and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
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13
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Beekman AM, O'Connell MA, Howell LA. Peptide-Directed Binding for the Discovery of Modulators of α-Helix-Mediated Protein-Protein Interactions: Proof-of-Concept Studies with the Apoptosis Regulator Mcl-1. Angew Chem Int Ed Engl 2017; 56:10446-10450. [PMID: 28670766 PMCID: PMC5577515 DOI: 10.1002/anie.201705008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Revised: 06/15/2017] [Indexed: 02/02/2023]
Abstract
Targeting PPIs with small molecules can be challenging owing to large, hydrophobic binding surfaces. Herein, we describe a strategy that exploits selective α-helical PPIs, transferring these characteristics to small molecules. The proof of concept is demonstrated with the apoptosis regulator Mcl-1, commonly exploited by cancers to avoid cell death. Peptide-directed binding uses few synthetic transformations, requires the production of a small number of compounds, and generates a high percentage of hits. In this example, about 50 % of the small molecules prepared showed an IC50 value of less than 100 μm, and approximately 25 % had IC50 values below 1 μm to Mcl-1. Compounds show selectivity for Mcl-1 over other anti-apoptotic proteins, possess cytotoxicity to cancer cell lines, and induce hallmarks of apoptosis. This approach represents a novel and economic process for the rapid discovery of new α-helical PPI modulators.
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Affiliation(s)
- Andrew Michael Beekman
- School of PharmacyUniversity of East AngliaNorwich Research Park, NorwichNorfolkNR4 7TJUK
| | - Maria Anne O'Connell
- School of PharmacyUniversity of East AngliaNorwich Research Park, NorwichNorfolkNR4 7TJUK
| | - Lesley Ann Howell
- School of PharmacyUniversity of East AngliaNorwich Research Park, NorwichNorfolkNR4 7TJUK
- School of Biological and Chemical SciencesQueen Mary University of LondonMile End RoadLondonE1 4NSUK
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14
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Beekman AM, O'Connell MA, Howell LA. Peptide-Directed Binding for the Discovery of Modulators of α-Helix-Mediated Protein-Protein Interactions: Proof-of-Concept Studies with the Apoptosis Regulator Mcl-1. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Andrew Michael Beekman
- School of Pharmacy; University of East Anglia; Norwich Research Park, Norwich Norfolk NR4 7TJ UK
| | - Maria Anne O'Connell
- School of Pharmacy; University of East Anglia; Norwich Research Park, Norwich Norfolk NR4 7TJ UK
| | - Lesley Ann Howell
- School of Pharmacy; University of East Anglia; Norwich Research Park, Norwich Norfolk NR4 7TJ UK
- School of Biological and Chemical Sciences; Queen Mary University of London; Mile End Road London E1 4NS UK
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15
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Burslem GM, Kyle HF, Nelson A, Edwards TA, Wilson AJ. Hypoxia inducible factor (HIF) as a model for studying inhibition of protein-protein interactions. Chem Sci 2017; 8:4188-4202. [PMID: 28878873 PMCID: PMC5576430 DOI: 10.1039/c7sc00388a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/31/2017] [Indexed: 12/21/2022] Open
Abstract
The state of the art in identifying protein–protein interaction inhibitors of hypoxia inducible factor – a promising target for anticancer drug design – is described.
The modulation of protein–protein interactions (PPIs) represents a major challenge in modern chemical biology. Current approaches (e.g. high-throughput screening, computer aided ligand design) are recognised as having limitations in terms of identification of hit matter. Considerable success has been achieved in terms of developing new approaches to PPI modulator discovery using the p53/hDM2 and Bcl-2 family of PPIs. However these important targets in oncology might be considered as “low-hanging-fruit”. Hypoxia inducible factor (HIF) is an emerging, but not yet fully validated target for cancer chemotherapy. Its role is to regulate the hypoxic response and it does so through a plethora of protein–protein interactions of varying topology, topography and complexity: its modulation represents an attractive approach to prevent development of new vasculature by hypoxic tumours.
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Affiliation(s)
- George M Burslem
- 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
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Adam Nelson
- 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
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK.,School of Molecular and Cellular Biology , Faculty of Biological Sciences , 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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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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