1
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Li X, He A, Liu Y, Huang Y, Zhang X. Bioinformatics identification of ferroptosis-related genes and therapeutic drugs in rheumatoid arthritis. Front Med (Lausanne) 2023; 10:1192153. [PMID: 37521346 PMCID: PMC10374025 DOI: 10.3389/fmed.2023.1192153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 06/19/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction Rheumatoid arthritis (RA) is a chronic immune disease characterized by synovial inflammation and bone destruction, with a largely unclear etiology. Evidence has indicated that ferroptosis may play an increasingly important role in the onset and development of RA. However, ferroptosis-related genes are still largely unexplored in RA. Therefore, this work focused on identifying and validating the potential ferroptosis-related genes involved in RA through bioinformatics analysis. Methods We screened differentially expressed ferroptosis-related genes (DEFGs) between RA patients and healthy individuals based on GSE55235 dataset. Subsequently, correlation analysis, protein-protein interaction (PPI) network analysis, GO, and KEGG enrichment analyses were performed using these DEFGs. Finally, our results were validated by GSE12021 dataset. Results We discovered 34 potential DEFGs in RA based on bioinformatics analysis. According to functional enrichment analysis, these genes were mainly enriched in HIF-1 signaling pathway, FoxO signaling pathway, and Ferroptosis pathway. Four genes (GABARPL1, DUSP1, JUN, and MAPK8) were validated to be downregulated by GSE12021 dataset and were diagnostic biomarkers and therapeutic targets for RA via the regulation of ferroptosis. Discussion Our results help shed more light on the pathogenesis of RA. Ferroptosis-related genes in RA are valuable diagnostic biomarkers and they will be exploited clinically as therapeutic targets in the future.
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Affiliation(s)
- Xianbin Li
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, Guangdong, China
- School of Computer Science of Information Technology, Qiannan Normal University for Nationalities, Duyun, Guizhou, China
| | - Andong He
- Department of Respiratory and Critical Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Yue Liu
- Institute of Computational Science and Technology, Guangzhou University, Guangzhou, Guangdong, China
| | - Yuye Huang
- Department of Respiratory and Critical Medicine, Ningbo First Hospital, Ningbo, Zhejiang, China
| | - Xueli Zhang
- Department of Medical Technology, Zhengzhou Railway Vocational and Technical College, Zhengzhou, Henan, China
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2
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Brennan A, Leech JT, Kad NM, Mason JM. The effect of helix-inducing constraints and downsizing upon a transcription block survival-derived functional cJun antagonist. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101077. [PMID: 36274790 PMCID: PMC9582194 DOI: 10.1016/j.xcrp.2022.101077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Inhibition of cJun is established as a promising therapeutic approach, particularly in cancer. We recently developed the "transcription block survival" (TBS) screening platform to derive functional peptide antagonists of transcription factor activity by ablating their ability to bind to cognate DNA. Using TBS, we screened a >131,000-member peptide library to select a 63-mer peptide that bound cJun and prevented 12-O-tetradecanoylphorbol-13-acetate response element (TRE) DNA binding. Iterative truncation was next combined with a systematic exploration of side-chain cyclization to derive a minimal active sequence. The resulting dual lactamized sequence was >40% smaller and retained low nM target affinity (equilibrium binding constant [K D ] = 0.2 versus 9.7 nM), with 8 residues at the acidic region required for functional antagonism. However, even modest C-terminal truncation resulted in functional loss. The peptide functionally antagonizes cJun (half-maximal inhibitory concentration [IC50] = 13 versus 45 μM) and is considerably more stable in human serum relative to its non-lactamized counterpart and HingeW.
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Affiliation(s)
- Andrew Brennan
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - James T. Leech
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
| | - Neil M. Kad
- School of Biological Sciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M. Mason
- Department of Life Sciences, University of Bath, Bath BA2 7AY, UK
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3
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Cobos C, Bansal PS, Wilson DT, Jones L, Zhao G, Field MA, Eichenberger RM, Pickering DA, Ryan RYM, Ratnatunga CN, Miles JJ, Ruscher R, Giacomin PR, Navarro S, Loukas A, Daly NL. Peptides derived from hookworm anti-inflammatory proteins suppress inducible colitis in mice and inflammatory cytokine production by human cells. Front Med (Lausanne) 2022; 9:934852. [PMID: 36186812 PMCID: PMC9524151 DOI: 10.3389/fmed.2022.934852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/25/2022] [Indexed: 11/21/2022] Open
Abstract
A decline in the prevalence of parasites such as hookworms appears to be correlated with the rise in non-communicable inflammatory conditions in people from high- and middle-income countries. This correlation has led to studies that have identified proteins produced by hookworms that can suppress inflammatory bowel disease (IBD) and asthma in animal models. Hookworms secrete a family of abundant netrin-domain containing proteins referred to as AIPs (Anti-Inflammatory Proteins), but there is no information on the structure-function relationships. Here we have applied a downsizing approach to the hookworm AIPs to derive peptides of 20 residues or less, some of which display anti-inflammatory effects when co-cultured with human peripheral blood mononuclear cells and oral therapeutic activity in a chemically induced mouse model of acute colitis. Our results indicate that a conserved helical region is responsible, at least in part, for the anti-inflammatory effects. This helical region has potential in the design of improved leads for treating IBD and possibly other inflammatory conditions.
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Affiliation(s)
- Claudia Cobos
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paramjit S. Bansal
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - David T. Wilson
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Linda Jones
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Guangzu Zhao
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Matthew A. Field
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Ramon M. Eichenberger
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Darren A. Pickering
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Rachael Y. M. Ryan
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Champa N. Ratnatunga
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - John J. Miles
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Roland Ruscher
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Paul R. Giacomin
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
| | - Severine Navarro
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Infection and Inflammation Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Faculty of Health, Woolworths Centre for Childhood Nutrition Research, Queensland University of Technology, South Brisbane, QLD, Australia
| | - Alex Loukas
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- *Correspondence: Alex Loukas,
| | - Norelle L. Daly
- Centre for Molecular Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, QLD, Australia
- Norelle L. Daly,
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Gaucher J, Reille‐Seroussi M, Broussy S. Structural and ITC Characterization of Peptide-Protein Binding: Thermodynamic Consequences of Cyclization Constraints, a Case Study on Vascular Endothelial Growth Factor Ligands. Chemistry 2022; 28:e202200465. [PMID: 35665969 PMCID: PMC9543606 DOI: 10.1002/chem.202200465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Indexed: 11/10/2022]
Abstract
Macrocyclization constraints are widely used in the design of protein ligands to stabilize their bioactive conformation and increase their affinities. However, the resulting changes in binding entropy can be puzzling and uncorrelated to affinity gains. Here, the thermodynamic (Isothermal Titration Calorimetry) and structural (X-ray, NMR and CD) analysis of a complete series of lactam-bridged peptide ligands of the vascular endothelial growth factor, and their unconstrained analogs are reported. It is shown that differences in thermodynamics arise mainly from the folding energy of the peptide upon binding. The systematic reduction in conformational entropy penalty due to helix pre-organization can be counterbalanced by an unfavorable vibrational entropy change if the constraints are too rigid. The gain in configurational entropy partially escapes the enthalpy/entropy compensation and leads to an improvement in affinity. The precision of the analytical ITC method makes this study a possible benchmark for constrained peptides optimization.
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Affiliation(s)
- Jean‐François Gaucher
- CiTCoMUMR CNRS 8038Université Paris Cité, Faculté de Santé, UFR de Pharmacie4 av. de l'Observatoire75006ParisFrance
| | - Marie Reille‐Seroussi
- CitCoMUMR CNRS 8038U1268 INSERMUniversité Paris Cité, Faculté de Santé, UFR de Pharmacie4 av. de l'Observatoire75006ParisFrance
| | - Sylvain Broussy
- CitCoMUMR CNRS 8038U1268 INSERMUniversité Paris Cité, Faculté de Santé, UFR de Pharmacie4 av. de l'Observatoire75006ParisFrance
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In vitro single molecule and bulk phase studies reveal the AP-1 transcription factor cFos binds to DNA without its partner cJun. J Biol Chem 2022; 298:102229. [PMID: 35787376 PMCID: PMC9364023 DOI: 10.1016/j.jbc.2022.102229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/27/2022] [Accepted: 06/29/2022] [Indexed: 11/23/2022] Open
Abstract
The AP-1 transcription factor family crucially regulates progression of the cell cycle, as well as playing roles in proliferation, differentiation, and the stress response. The two best described AP-1 family members, cFos and cJun, are known to dimerize to form a functional AP-1 heterodimer that binds to a consensus response element sequence. Although cJun can also homodimerize and bind to DNA, the canonical view is that cFos cannot bind DNA without heterodimerizing with cJun. Here, we show that cFos can actually bind to DNA in the absence of cJun in vitro. Using dual color single molecule imaging of cFos alone, we directly visualize binding to and movement on DNA. Of all these DNA-bound proteins, detailed analysis suggested 30 to 46% were homodimers. Furthermore, we constructed fluorescent protein fusions of cFos and cJun for Förster resonance energy transfer experiments. These constructs indicated complete dimerization of cJun, but although cFos could dimerize, its extent was reduced. Finally, to provide orthogonal confirmation of cFos binding to DNA, we performed bulk-phase circular dichroism experiments that showed clear structural changes in DNA; these were found to be specific to the AP-1 consensus sequence. Taken together, our results clearly show cFos can interact with DNA both as monomers and dimers independently of its archetypal partner, cJun.
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6
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Tian Y, Tirrell MV, LaBelle JL. Harnessing the Therapeutic Potential of Biomacromolecules through Intracellular Delivery of Nucleic Acids, Peptides, and Proteins. Adv Healthc Mater 2022; 11:e2102600. [PMID: 35285167 PMCID: PMC9232950 DOI: 10.1002/adhm.202102600] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 02/09/2022] [Indexed: 12/19/2022]
Abstract
Biomacromolecules have long been at the leading edge of academic and pharmaceutical drug development and clinical translation. With the clinical advances of new therapeutics, such as monoclonal antibodies and nucleic acids, the array of medical applications of biomacromolecules has broadened considerably. A major on-going effort is to expand therapeutic targets within intracellular locations. Owing to their large sizes, abundant charges, and hydrogen-bond donors and acceptors, advanced delivery technologies are required to deliver biomacromolecules effectively inside cells. In this review, strategies used for the intracellular delivery of three major forms of biomacromolecules: nucleic acids, proteins, and peptides, are highlighted. An emphasis is placed on synthetic delivery approaches and the major hurdles needed to be overcome for their ultimate clinical translation.
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Affiliation(s)
- Yu Tian
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 S Ellis Ave, Chicago, IL, 60637, USA
| | - Matthew V Tirrell
- Pritzker School of Molecular Engineering, The University of Chicago, 5640 S Ellis Ave, Chicago, IL, 60637, USA
| | - James L LaBelle
- Department of Pediatrics, Section of Hematology/Oncology, The University of Chicago, 900 E 57th St, Chicago, IL, 60637, USA
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7
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Casalino L, Talotta F, Cimmino A, Verde P. The Fra-1/AP-1 Oncoprotein: From the "Undruggable" Transcription Factor to Therapeutic Targeting. Cancers (Basel) 2022; 14:cancers14061480. [PMID: 35326630 PMCID: PMC8946526 DOI: 10.3390/cancers14061480] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 02/06/2023] Open
Abstract
The genetic and epigenetic changes affecting transcription factors, coactivators, and chromatin modifiers are key determinants of the hallmarks of cancer. The acquired dependence on oncogenic transcriptional regulators, representing a major determinant of cancer cell vulnerability, points to transcription factors as ideal therapeutic targets. However, given the unavailability of catalytic activities or binding pockets for small-molecule inhibitors, transcription factors are generally regarded as undruggable proteins. Among components of the AP-1 complex, the FOS-family transcription factor Fra-1, encoded by FOSL1, has emerged as a prominent therapeutic target. Fra-1 is overexpressed in most solid tumors, in response to the BRAF-MAPK, Wnt-beta-catenin, Hippo-YAP, IL-6-Stat3, and other major oncogenic pathways. In vitro functional analyses, validated in onco-mouse models and corroborated by prognostic correlations, show that Fra-1-containing dimers control tumor growth and disease progression. Fra-1 participates in key mechanisms of cancer cell invasion, Epithelial-to-Mesenchymal Transition, and metastatic spreading, by driving the expression of EMT-inducing transcription factors, cytokines, and microRNAs. Here we survey various strategies aimed at inhibiting tumor growth, metastatic dissemination, and drug resistance by interfering with Fra-1 expression, stability, and transcriptional activity. We summarize several tools aimed at the design and tumor-specific delivery of Fra-1/AP-1-specific drugs. Along with RNA-based therapeutics targeting the FOSL1 gene, its mRNA, or cognate regulatory circRNAs, we will examine the exploitation of blocking peptides, small molecule inhibitors, and innovative Fra-1 protein degraders. We also consider the possible caveats concerning Fra-1 inhibition in specific therapeutic contexts. Finally, we discuss a recent suicide gene therapy-based approach, aimed at selectively killing the Fra-1-overexpressing neoplastic cells.
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Affiliation(s)
- Laura Casalino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
| | | | - Amelia Cimmino
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
| | - Pasquale Verde
- Institute of Genetics and Biophysics “Adriano Buzzati Traverso”, Consiglio Nazionale dele Ricerche (CNR), 80131 Naples, Italy;
- Correspondence: (L.C.); (P.V.)
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8
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Buyanova M, Pei D. Targeting intracellular protein-protein interactions with macrocyclic peptides. Trends Pharmacol Sci 2022; 43:234-248. [PMID: 34911657 PMCID: PMC8840965 DOI: 10.1016/j.tips.2021.11.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/23/2021] [Accepted: 11/09/2021] [Indexed: 01/07/2023]
Abstract
Intracellular protein-protein interactions (PPIs) are challenging targets for traditional drug modalities. Macrocyclic peptides (MPs) prove highly effective PPI inhibitors in vitro and can be rapidly discovered against PPI targets by rational design or screening combinatorial libraries but are generally impermeable to the cell membrane. Recent advances in MP science and technology are allowing for the development of 'drug-like' MPs that potently and specifically modulate intracellular PPI targets in cell culture and animal models. In this review, we highlight recent progress in generating cell-permeable MPs that enter the mammalian cell by passive diffusion, endocytosis followed by endosomal escape, or as-yet unknown mechanisms.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA.
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9
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Fan F, Podar K. The Role of AP-1 Transcription Factors in Plasma Cell Biology and Multiple Myeloma Pathophysiology. Cancers (Basel) 2021; 13:2326. [PMID: 34066181 PMCID: PMC8151277 DOI: 10.3390/cancers13102326] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/02/2021] [Accepted: 05/06/2021] [Indexed: 12/19/2022] Open
Abstract
Multiple myeloma (MM) is an incurable hematologic malignancy characterized by the clonal expansion of malignant plasma cells within the bone marrow. Activator Protein-1 (AP-1) transcription factors (TFs), comprised of the JUN, FOS, ATF and MAF multigene families, are implicated in a plethora of physiologic processes and tumorigenesis including plasma cell differentiation and MM pathogenesis. Depending on the genetic background, the tumor stage, and cues of the tumor microenvironment, specific dimeric AP-1 complexes are formed. For example, AP-1 complexes containing Fra-1, Fra-2 and B-ATF play central roles in the transcriptional control of B cell development and plasma cell differentiation, while dysregulation of AP-1 family members c-Maf, c-Jun, and JunB is associated with MM cell proliferation, survival, drug resistance, bone marrow angiogenesis, and bone disease. The present review article summarizes our up-to-date knowledge on the role of AP-1 family members in plasma cell differentiation and MM pathophysiology. Moreover, it discusses novel, rationally derived approaches to therapeutically target AP-1 TFs, including protein-protein and protein-DNA binding inhibitors, epigenetic modifiers and natural products.
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Affiliation(s)
- Fengjuan Fan
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue 1277, Wuhan 430022, China;
| | - Klaus Podar
- Department of Internal Medicine II, University Hospital Krems, Mitterweg 10, 3500 Krems an der Donau, Austria
- Molecular Oncology and Hematology Unit, Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Strasse 30, 3500 Krems an der Donau, Austria
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10
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Plaper T, Aupič J, Dekleva P, Lapenta F, Keber MM, Jerala R, Benčina M. Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion. Sci Rep 2021; 11:9136. [PMID: 33911109 PMCID: PMC8080620 DOI: 10.1038/s41598-021-88315-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 12/19/2022] Open
Abstract
Coiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range. In vitro stability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism of viral spike protein-mediated fusion or screening for viral inhibitors under biosafety level 1 conditions.
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Affiliation(s)
- Tjaša Plaper
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,Interfaculty Doctoral Study of Biomedicine, University of Ljubljana, Ljubljana, Slovenia
| | - Jana Aupič
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Petra Dekleva
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia
| | - Fabio Lapenta
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Mateja Manček Keber
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia.,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
| | - Mojca Benčina
- Department of Synthetic Biology and Immunology, National Institute of Chemistry, Hajdrihova 19, 1001, Ljubljana, Slovenia. .,EN-FIST Centre of Excellence, Trg Osvobodilne Fronte 13, 1000, Ljubljana, Slovenia.
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11
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Madden SK, de Araujo AD, Gerhardt M, Fairlie DP, Mason JM. Taking the Myc out of cancer: toward therapeutic strategies to directly inhibit c-Myc. Mol Cancer 2021; 20:3. [PMID: 33397405 PMCID: PMC7780693 DOI: 10.1186/s12943-020-01291-6] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 11/29/2020] [Indexed: 02/07/2023] Open
Abstract
c-Myc is a transcription factor that is constitutively and aberrantly expressed in over 70% of human cancers. Its direct inhibition has been shown to trigger rapid tumor regression in mice with only mild and fully reversible side effects, suggesting this to be a viable therapeutic strategy. Here we reassess the challenges of directly targeting c-Myc, evaluate lessons learned from current inhibitors, and explore how future strategies such as miniaturisation of Omomyc and targeting E-box binding could facilitate translation of c-Myc inhibitors into the clinic.
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Affiliation(s)
- Sarah K Madden
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC 1066 Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Mara Gerhardt
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC 1066 Centre of Excellence for Innovations in Peptide and Protein Science, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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12
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López‐García P, de Araujo AD, Bergues‐Pupo AE, Tunn I, Fairlie DP, Blank KG. Fortified Coiled Coils: Enhancing Mechanical Stability with Lactam or Metal Staples. Angew Chem Int Ed Engl 2021; 60:232-236. [PMID: 32940968 PMCID: PMC7821110 DOI: 10.1002/anie.202006971] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Indexed: 12/19/2022]
Abstract
Coiled coils (CCs) are powerful supramolecular building blocks for biomimetic materials, increasingly used for their mechanical properties. Here, we introduce helix-inducing macrocyclic constraints, so-called staples, to tune thermodynamic and mechanical stability of CCs. We show that thermodynamic stabilization of CCs against helix uncoiling primarily depends on the number of staples, whereas staple positioning controls CC mechanical stability. Inserting a covalent lactam staple at one key force application point significantly increases the barrier to force-induced CC dissociation and reduces structural deformity. A reversible His-Ni2+ -His metal staple also increases CC stability, but ruptures upon mechanical loading to allow helix uncoiling. Staple type, position and number are key design parameters in using helical macrocyclic templates for fine-tuning CC properties in emerging biomaterials.
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Affiliation(s)
- Patricia López‐García
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Aline D. de Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Ana E. Bergues‐Pupo
- Department of Theory and Bio-SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Present address: Berlin Institute for Medical Systems BiologyMax Delbrück Center for Molecular Medicine10115BerlinGermany
| | - Isabell Tunn
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - David P. Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein ScienceInstitute for Molecular BioscienceThe University of QueenslandBrisbaneQld4072Australia
| | - Kerstin G. Blank
- Mechano(bio)chemistryMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
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Lindsey‐Crosthwait A, Rodriguez‐Lema D, Walko M, Pask CM, Wilson AJ. Structural optimization of reversible dibromomaleimide peptide stapling. Pept Sci (Hoboken) 2021; 113:e24157. [PMID: 34938942 PMCID: PMC8650577 DOI: 10.1002/pep2.24157] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/29/2020] [Accepted: 03/02/2020] [Indexed: 01/05/2023]
Abstract
Methods to constrain peptides in a bioactive α-helical conformation for inhibition of protein-protein interactions represent an ongoing area of investigation in chemical biology. Recently, the first example of a reversible "stapling" methodology was described which exploits native cysteine or homocysteine residues spaced at the i and i + 4 positions in a peptide sequence together with the thiol selective reactivity of dibromomaleimides (a previous study). This manuscript reports on the optimization of the maleimide based constraint, focusing on the kinetics of macrocyclization and the extent to which helicity is promoted with different thiol containing amino acids. The study identified an optimal stapling combination of X 1 = L-Cys and X 5 = L-hCys in the context of the model peptide Ac-X1AAAX5-NH2, which should prove useful in implementing the dibromomaleimide stapling strategy in peptidomimetic ligand discovery programmes.
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Affiliation(s)
- Ayanna Lindsey‐Crosthwait
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Diana Rodriguez‐Lema
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | - Martin Walko
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
| | | | - Andrew J. Wilson
- School of Chemistry, University of LeedsLeedsUK
- Astbury Centre for Structural Molecular Biology, University of LeedsLeedsUK
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14
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Mu W, Jia Y, Chen X, Li H, Wang Z, Cheng B. Intracellular Porphyromonas gingivalis Promotes the Proliferation of Colorectal Cancer Cells via the MAPK/ERK Signaling Pathway. Front Cell Infect Microbiol 2020; 10:584798. [PMID: 33425779 PMCID: PMC7785964 DOI: 10.3389/fcimb.2020.584798] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Accepted: 11/20/2020] [Indexed: 12/11/2022] Open
Abstract
Porphyromonas gingivalis (P. gingivalis) is a keystone pathogen in periodontitis. However, several clinical studies have revealed an enrichment of P. gingivalis in the stool samples and colorectal mucosa of colorectal cancer patients. Thus, the goal of this study was to determine whether P. gingivalis can promote colorectal cancer progression in vitro. We established an acute infection model (24 h, multiplicity of infection =100) of P. gingivalis invasion of colorectal cancer cells to study the alterations induced by P. gingivalis in the proliferation and cell cycle of colorectal cancer cells. We observed that P. gingivalis can adhere and invade host cells a few hours after infection. Once invaded, P. gingivalis significantly promoted colorectal cancer cell proliferation, and the percentage of S phase cells was increased in the cell cycle assay. However, KDP136, a gingipain-deficient mutant of P. gingivalis 33277, showed a decreased ability to promote colorectal cancer cell proliferation, indicating that gingipain is associated with colorectal cancer cell proliferation. Furthermore, we extracted RNA from colorectal cancer cells for high-throughput sequencing analysis and reconfirmed the results by quantitative polymerase chain reaction and western blot analyses. The results suggested that the MAPK/ERK signaling pathway is significantly activated by P. gingivalis, while these changes were not observed for KDP136. In conclusion, P. gingivalis can invade cells and promote the proliferation of colorectal cancer cells by activating the MAPK/ERK signaling pathway. Gingipain is an essential virulence factor in this interaction.
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Affiliation(s)
- Wenxin Mu
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Yiqun Jia
- Stomatology Center, Shenzhen People's Hospital, The Second Clinical Medical College of Jinan University, The First Affiliated Hospital of Southern University of Science and Technology, Shenzhen, China
| | - Xiaobing Chen
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Haoyu Li
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Zhi Wang
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
| | - Bin Cheng
- Hospital of Stomatology, Guanghua School of Stomatology, Guangdong Provincial Key Laboratory of Stomatology, Sun Yat-Sen University, Guangzhou, China
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15
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López‐García P, Araujo AD, Bergues‐Pupo AE, Tunn I, Fairlie DP, Blank KG. Mechanische Verstärkung von Coiled Coils mit Lactam und Histidin‐Metall‐Klammern. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202006971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patricia López‐García
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
| | - Aline D. Araujo
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australien
| | - Ana E. Bergues‐Pupo
- Abteilung für Theorie und Bio-Systeme Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
- Aktuelle Adresse: Berlin Institute for Medical Systems Biology Max-Delbrück-Centrum für Molekulare Medizin 10115 Berlin Deutschland
| | - Isabell Tunn
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
| | - David P. Fairlie
- ARC Centre of Excellence for Innovations in Peptide and Protein Science Institute for Molecular Bioscience The University of Queensland Brisbane Qld 4072 Australien
| | - Kerstin G. Blank
- Mechano(bio)chemie Max-Planck-Institut für Kolloid- und Grenzflächenforschung Am Mühlenberg 1 14476 Potsdam Deutschland
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16
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Brennan A, Leech JT, Kad NM, Mason JM. Selective antagonism of cJun for cancer therapy. J Exp Clin Cancer Res 2020; 39:184. [PMID: 32917236 PMCID: PMC7488417 DOI: 10.1186/s13046-020-01686-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 08/20/2020] [Indexed: 01/10/2023] Open
Abstract
The activator protein-1 (AP-1) family of transcription factors modulate a diverse range of cellular signalling pathways into outputs which can be oncogenic or anti-oncogenic. The transcription of relevant genes is controlled by the cellular context, and in particular by the dimeric composition of AP-1. Here, we describe the evidence linking cJun in particular to a range of cancers. This includes correlative studies of protein levels in patient tumour samples and mechanistic understanding of the role of cJun in cancer cell models. This develops an understanding of cJun as a focal point of cancer-altered signalling which has the potential for therapeutic antagonism. Significant work has produced a range of small molecules and peptides which have been summarised here and categorised according to the binding surface they target within the cJun-DNA complex. We highlight the importance of selectively targeting a single AP-1 family member to antagonise known oncogenic function and avoid antagonism of anti-oncogenic function.
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Affiliation(s)
- Andrew Brennan
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - James T Leech
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Neil M Kad
- School of Biosciences, University of Kent, Canterbury, CT2 7NH, UK
| | - Jody M Mason
- Department of Biology & Biochemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
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17
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Baggio C, Udompholkul P, Gambini L, Jossart J, Salem AF, Håkansson M, Perry JJP, Pellecchia M. N-locking stabilization of covalent helical peptides: Application to Bfl-1 antagonists. Chem Biol Drug Des 2020; 95:412-426. [PMID: 31898401 DOI: 10.1111/cbdd.13661] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/16/2019] [Accepted: 12/23/2019] [Indexed: 12/15/2022]
Abstract
Recently, it was reported that tetrapeptides cyclized via lactam bond between the amino terminus and a glutamic residue in position 4 (termed here N-lock) can nucleate helix formation in longer peptides. We applied such strategy to derive N-locked covalent BH3 peptides that were designed to selectively target the anti-apoptotic protein Bfl-1. The resulting agents were soluble in aqueous buffer and displayed a remarkable (low nanomolar) affinity for Bfl-1 and cellular activity. The crystal structure of the complex between such N-locked covalent peptide and Bfl-1 provided insights on the geometry of the N-locking strategy and of the covalent bond between the agent and Bfl-1.
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Affiliation(s)
- Carlo Baggio
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Parima Udompholkul
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Luca Gambini
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | - Jennifer Jossart
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Ahmed F Salem
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
| | | | - J Jefferson P Perry
- Department of Biochemistry, College of Natural and Agricultural Sciences, University of California Riverside, Riverside, CA, USA
| | - Maurizio Pellecchia
- Division of Biomedical Sciences, School of Medicine, University of California Riverside, Riverside, CA, USA
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18
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Hoang HN, Wu C, Hill TA, Dantas de Araujo A, Bernhardt PV, Liu L, Fairlie DP. A Novel Long‐Range n to π* Interaction Secures the Smallest known α‐Helix in Water. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Huy N. Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Chongyang Wu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences The University of Queensland Brisbane Qld 4072 Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging Institute for Molecular Bioscience The University of Queensland Brisbane QLD 4072 Australia
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19
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Hoang HN, Wu C, Hill TA, Dantas de Araujo A, Bernhardt PV, Liu L, Fairlie DP. A Novel Long-Range n to π* Interaction Secures the Smallest known α-Helix in Water. Angew Chem Int Ed Engl 2019; 58:18873-18877. [PMID: 31625253 DOI: 10.1002/anie.201911277] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 10/10/2019] [Indexed: 12/17/2022]
Abstract
The introduction of an amide bond linking side chains of the first and fifth amino acids forms a cyclic pentapeptide that optimally stabilizes the smallest known α-helix in water. The origin of the stabilization is unclear. The observed dependence of α-helicity on the solvent and cyclization linker led us to discover a novel long-range n to π* interaction between a main-chain amide oxygen and a uniquely positioned carbonyl group in the linker of cyclic pentapeptides. CD and NMR spectra, NMR and X-ray structures, modelling, and MD simulations reveal that this first example of a synthetically incorporated long-range n to π* CO⋅⋅⋅Cγ =Ο interaction uniquely enforces an almost perfect and remarkably stable peptide α-helix in water but not in DMSO. This unusual interaction with a covalent amide bond outside the helical backbone suggests new approaches to synthetically stabilize peptide structures in water.
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Affiliation(s)
- Huy N Hoang
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Chongyang Wu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Timothy A Hill
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Aline Dantas de Araujo
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Paul V Bernhardt
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Ligong Liu
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - David P Fairlie
- Division of Chemistry and Structural Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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20
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Lathbridge A, Mason JM. Combining Constrained Heptapeptide Cassettes with Computational Design To Create Coiled-Coil Targeting Helical Peptides. ACS Chem Biol 2019; 14:1293-1304. [PMID: 31117396 DOI: 10.1021/acschembio.9b00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A total of 32 heptapeptides have been synthesized and characterized to establish the effect of K → D (i → i + 4) lactamization upon their ability to adopt a helical conformation. Because most parallel and dimeric coiled-coil sequences can be deconvoluted into gabcdef repeats, we have introduced fixed solvent exposed b → f (K → D) constraints into this design scaffold. Interfacial " a" hydrophobic (L/I/V/N) and " e/g" electrostatic (E/K) options (4 × 2 × 2 = 16 cassettes) were introduced as core drivers of coiled-coil stability and specificity. All present as random coils when linear but adopt a helical conformation upon lactamization. Helicity varied in magnitude from 34 to 68%, indicating different levels of constraint tolerance within the context of a sequence required to be helical for function. Using the oncogenic transcription factor cJun as an exemplar, we next utilized our bCIPA coiled-coil screening engine to select four cassettes of highest predicted affinity when paired with four gabcdef cassettes within the full-length cJun target counterpart (164 = 65 536 combinations). This information was coupled with observed helicity for each constrained cassette to select for the best balance of predicted affinity when linear and experimentally validated helicity when constrained. As a control, the same approach was taken using cassettes of high predicted target affinity but with lower experimentally validated helicity. The approach provides a novel platform of modular heptapeptide cassettes experimentally validated and separated by helical content. Appropriate cassettes can be selected and conjugated to produce longer peptides, in which constraints impart appropriate helicity such that a wide range of targets can be engaged with high affinity and selectivity.
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21
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Bakail M, Rodriguez‐Marin S, Hegedüs Z, Perrin ME, Ochsenbein F, Wilson AJ. Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides. Chembiochem 2019; 20:891-895. [PMID: 30512234 PMCID: PMC6468270 DOI: 10.1002/cbic.201800633] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Indexed: 12/20/2022]
Abstract
Inhibiting the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α-helix-mediated PPI, constraining the key histone H3 helix (residues 118-135) is a strategy through which chemical probes might be elaborated to test this hypothesis. In this work, variant H3118-135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophysical analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs.
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Affiliation(s)
- May Bakail
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
- Present address: Inserm, U1016Institut CochinCNRSUMR8104Université Paris Descartes27, rue du Faubourg Saint-Jacques75014ParisFrance
| | - Silvia Rodriguez‐Marin
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Zsófia Hegedüs
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
| | - Marie E. Perrin
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Françoise Ochsenbein
- Institute for Integrative Biology of the Cell (I2BC)IBITECSCEACNRSUniversité Paris–SudUniversité Paris–Saclay91198Gif-sur-Yvette CedexFrance
| | - Andrew J. Wilson
- School of ChemistryUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsWoodhouse LaneLeedsLS2 9JTUK
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22
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Roy S, Ghosh P, Ahmed I, Chakraborty M, Naiya G, Ghosh B. Constrained α-Helical Peptides as Inhibitors of Protein-Protein and Protein-DNA Interactions. Biomedicines 2018; 6:E118. [PMID: 30567318 PMCID: PMC6315407 DOI: 10.3390/biomedicines6040118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 02/06/2023] Open
Abstract
Intracellular regulatory pathways are replete with protein-protein and protein-DNA interactions, offering attractive targets for therapeutic interventions. So far, most drugs are targeted toward enzymes and extracellular receptors. Protein-protein and protein-DNA interactions have long been considered as "undruggable". Protein-DNA interactions, in particular, present a difficult challenge due to the repetitive nature of the B-DNA. Recent studies have provided several breakthroughs; however, a design methodology for these classes of inhibitors is still at its infancy. A dominant motif of these macromolecular interactions is an α-helix, raising possibilities that an appropriate conformationally-constrained α-helical peptide may specifically disrupt these interactions. Several methods for conformationally constraining peptides to the α-helical conformation have been developed, including stapling, covalent surrogates of hydrogen bonds and incorporation of unnatural amino acids that restrict the conformational space of the peptide. We will discuss these methods and several case studies where constrained α-helices have been used as building blocks for appropriate molecules. Unlike small molecules, the delivery of these short peptides to their targets is not straightforward as they may possess unfavorable cell penetration and ADME properties. Several methods have been developed in recent times to overcome some of these problems. We will discuss these issues and the prospects of this class of molecules as drugs.
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Affiliation(s)
- Siddhartha Roy
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Piya Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Israr Ahmed
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Madhumita Chakraborty
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Gitashri Naiya
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
| | - Basusree Ghosh
- Department of Biophysics, Bose Institute, P1/12 CIT Scheme VII M, Kolkata 700054, India.
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23
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Han Y, Zhao X, Sun Y, Sui Y, Liu J. Retracted
: Effects of FOSL1 silencing on osteosarcoma cell proliferation, invasion and migration through the ERK/AP‐1 signaling pathway. J Cell Physiol 2018; 234:3598-3612. [DOI: 10.1002/jcp.27048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Accepted: 06/26/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Yu Han
- Joint Surgery Department No.1 Hospital of Jilin University Changchun China
| | - Xingyu Zhao
- Joint Surgery Department No.1 Hospital of Jilin University Changchun China
| | - Yifu Sun
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences Beijing China
| | - Yutong Sui
- Jilin Provincial Key Laboratory for Molecular Biology of Special Economic Animals Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences Beijing China
| | - Jianguo Liu
- Joint Surgery Department No.1 Hospital of Jilin University Changchun China
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24
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Recent Studies on Ponatinib in Cancers Other Than Chronic Myeloid Leukemia. Cancers (Basel) 2018; 10:cancers10110430. [PMID: 30423915 PMCID: PMC6267038 DOI: 10.3390/cancers10110430] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/24/2018] [Accepted: 11/07/2018] [Indexed: 02/08/2023] Open
Abstract
Ponatinib is a third line drug for the treatment of chronic myeloid leukemia patients, especially those that develop the gatekeeper mutation T315I, which is resistant to the first and the second line drugs imatinib, nilotinib, dasatinib and bosutinib. The compound was first identified as a pan Bcr-Abl and Src kinase inhibitor. Further studies have indicated that it is a multitargeted inhibitor that is active on FGFRs, RET, AKT, ERK1/2, KIT, MEKK2 and other kinases. For this reason, the compound has been evaluated on several cancers in which these kinases play important roles, including thyroid, breast, ovary and lung cancer, neuroblastoma, rhabdoid tumours and in myeloproliferative disorders. Ponatinib is also being tested in clinical trials to evaluate its activity in FLT3-ITD acute myelogenous leukemia, head and neck cancers, certain type of lung cancer, gastrointestinal stromal tumours and other malignancies. In this review we report the most recent preclinical and clinical studies on ponatinib in cancers other than CML, with the aim of giving a complete overview of this interesting compound.
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25
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Lathbridge A, Mason JM. Computational Competitive and Negative Design To Derive a Specific cJun Antagonist. Biochemistry 2018; 57:6108-6118. [PMID: 30256622 DOI: 10.1021/acs.biochem.8b00782] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Basic leucine zipper (bZIP) proteins reside at the end of cell-signaling cascades and function to modulate transcription of specific gene targets. bZIPs are recognized as important regulators of cellular processes such as cell growth, apoptosis, and cell differentiation. One such validated transcriptional regulator, activator protein-1, is typically comprised of heterodimers of Jun and Fos family members and is key in the progression and development of a number of different diseases. The best described component, cJun, is upregulated in a variety of diseases such as cancer, osteoporosis, and psoriasis. Toward our goal of inhibiting bZIP proteins implicated in disease pathways, we here describe the first use of a novel in silico peptide library screening platform that facilitates the derivation of sequences exhibiting a high affinity for cJun while disfavoring homodimer formation or formation of heterodimers with other closely related Fos sequences. In particular, using Fos as a template, we have computationally screened a peptide library of more than 60 million members and ranked hypothetical on/off target complexes according to predicted stability. This resulted in the identification of a sequence that bound cJun but displayed little homomeric stability or preference for cFos. The computationally selected sequence maintains an interaction stability similar to that of a previous experimentally derived cJun antagonist while providing much improved specificity. Our study provides new insight into the use of tandem in silico screening/ in vitro validation and the ability to create a peptide that is capable of satisfying conflicting design requirements.
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Affiliation(s)
- Alexander Lathbridge
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , U.K
| | - Jody M Mason
- Department of Biology & Biochemistry , University of Bath , Claverton Down , Bath BA2 7AY , U.K
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26
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Baxter D, Ullman CG, Frigotto L, Mason JM. Exploiting Overlapping Advantages of In Vitro and In Cellulo Selection Systems to Isolate a Novel High-Affinity cJun Antagonist. ACS Chem Biol 2017; 12:2579-2588. [PMID: 28880076 DOI: 10.1021/acschembio.7b00693] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have combined two peptide library-screening systems, exploiting the benefits offered by both to select novel antagonistic agents of cJun. CIS display is an in vitro cell-free system that allows very large libraries (≤1014) to be interrogated. However, affinity-based screening conditions can poorly reflect those relevant to therapeutic application, particularly for difficult intracellular targets, and can lead to false positives. In contrast, an in cellulo screening system such as the Protein-fragment Complementation Assay (PCA) selects peptides with high target affinity while additionally profiling for target specificity, protease resistance, solubility, and lack of toxicity in a more relevant context. A disadvantage is the necessity to transform cells, limiting library sizes that can be screened to ≤106. However, by combining both cell-free and cell-based systems, we isolated a peptide (CPW) from a ∼1010 member library, which forms a highly stable interaction with cJun (Tm = 63 °C, Kd = 750 nM, ΔG = -8.2 kcal/mol) using the oncogenic transcriptional regulator Activator Protein-1 (AP-1) as our exemplar target. In contrast, CIS display alone selected a peptide with low affinity for cJun (Tm = 34 °C, Kd = 25 μM, ΔG = -6.2 kcal/mol), highlighting the benefit of CIS → PCA. Furthermore, increased library size with CIS → PCA vs PCA alone allows the freedom to introduce noncanonical options, such as interfacial aromatics, and solvent exposed options that may allow the molecule to explore alternative structures and interact with greater affinity and efficacy with the target. CIS → PCA therefore offers significant potential as a peptide-library screening platform by synergistically combining the relative attributes of both assays to generate therapeutically interesting compounds that may otherwise not be identified.
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Affiliation(s)
- Daniel Baxter
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Christopher G. Ullman
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Laura Frigotto
- Isogenica Ltd., Chesterford Research
Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jody M. Mason
- Dept
of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom
| |
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