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Xu MY, Zeng N, Liu CQ, Sun JX, An Y, Zhang SH, Xu JZ, Zhong XY, Ma SY, He HD, Hu J, Xia QD, Wang SG. Enhanced cellular therapy: revolutionizing adoptive cellular therapy. Exp Hematol Oncol 2024; 13:47. [PMID: 38664743 PMCID: PMC11046957 DOI: 10.1186/s40164-024-00506-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 03/31/2024] [Indexed: 04/28/2024] Open
Abstract
Enhanced cellular therapy has emerged as a novel concept following the basis of cellular therapy. This treatment modality applied drugs or biotechnology to directly enhance or genetically modify cells to enhance the efficacy of adoptive cellular therapy (ACT). Drugs or biotechnology that enhance the killing ability of immune cells include immune checkpoint inhibitors (ICIs) / antibody drugs, small molecule inhibitors, immunomodulatory factors, proteolysis targeting chimera (PROTAC), oncolytic virus (OV), etc. Firstly, overcoming the inhibitory tumor microenvironment (TME) can enhance the efficacy of ACT, which can be achieved by blocking the immune checkpoint. Secondly, cytokines or cytokine receptors can be expressed by genetic engineering or added directly to adoptive cells to enhance the migration and infiltration of adoptive cells to tumor cells. Moreover, multi-antigen chimeric antigen receptors (CARs) can be designed to enhance the specific recognition of tumor cell-related antigens, and OVs can also stimulate antigen release. In addition to inserting suicide genes into adoptive cells, PROTAC technology can be used as a safety switch or degradation agent of immunosuppressive factors to enhance the safety and efficacy of adoptive cells. This article comprehensively summarizes the mechanism, current situation, and clinical application of enhanced cellular therapy, describing potential improvements to adoptive cellular therapy.
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Affiliation(s)
- Meng-Yao Xu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Na Zeng
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Chen-Qian Liu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jian-Xuan Sun
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Ye An
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Si-Han Zhang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jin-Zhou Xu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Xing-Yu Zhong
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Si-Yang Ma
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Hao-Dong He
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Jia Hu
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China
| | - Qi-Dong Xia
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China.
| | - Shao-Gang Wang
- Department and Institute of Urology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No.1095 Jiefang Avenue, Wuhan, 430030, China.
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2
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Tarantino A, Ciconte G, Ghiroldi A, Mastrocinque F, Micaglio E, Boccellino A, Negro G, Piccoli M, Cirillo F, Vicedomini G, Santinelli V, Anastasia L, Pappone C. Challenges in Brugada Syndrome Stratification: Investigating SCN5A Mutation Localization and Clinical Phenotypes. Int J Mol Sci 2023; 24:16658. [PMID: 38068978 PMCID: PMC10706434 DOI: 10.3390/ijms242316658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 11/15/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
Brugada Syndrome (BrS) is a genetic heart condition linked to sudden cardiac death. Though the SCN5A gene is primarily associated with BrS, there is a lack of comprehensive studies exploring the connection between SCN5A mutation locations and the clinical presentations of the syndrome. This study aimed to address this gap and gain further understanding of the syndrome. The investigation classified 36 high-risk BrS patients based on SCN5A mutations within the transmembrane/structured (TD) and intra-domain loops (IDLs) lacking a 3D structure. We characterized the intrinsically disordered regions (IDRs) abundant in IDLs, using bioinformatics tools to predict IDRs and post-translational modifications (PTMs) in NaV1.5. Interestingly, it was found that current predictive tools often underestimate the impacts of mutations in IDLs and disordered regions. Moreover, patients with SCN5A mutations confined to IDL regions-previously deemed 'benign'-displayed clinical symptoms similar to those carrying 'damaging' variants. Our research illuminates the difficulty in stratifying patients based on SCN5A mutation locations, emphasizing the vital role of IDLs in the NaV1.5 channel's functioning and protein interactions. We advocate for caution when using predictive tools for mutation evaluation in these regions and call for the development of improved strategies in accurately assessing BrS risk.
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Affiliation(s)
- Adriana Tarantino
- Institute for Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (A.T.); (M.P.); (F.C.)
- School of Medicine, University Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy;
| | - Giuseppe Ciconte
- School of Medicine, University Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy;
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Andrea Ghiroldi
- Institute for Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (A.T.); (M.P.); (F.C.)
| | - Flavio Mastrocinque
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Emanuele Micaglio
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Antonio Boccellino
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Gabriele Negro
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Marco Piccoli
- Institute for Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (A.T.); (M.P.); (F.C.)
| | - Federica Cirillo
- Institute for Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (A.T.); (M.P.); (F.C.)
| | - Gabriele Vicedomini
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Vincenzo Santinelli
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
| | - Luigi Anastasia
- Institute for Molecular and Translational Cardiology (IMTC), IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (A.T.); (M.P.); (F.C.)
- School of Medicine, University Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy;
| | - Carlo Pappone
- School of Medicine, University Vita-Salute San Raffaele, Via Olgettina 58, 20132 Milan, Italy;
- Arrhythmology Department, IRCCS Policlinico San Donato, Piazza Malan 2, San Donato Milanese, 20097 Milan, Italy; (F.M.); (E.M.); (A.B.); (G.N.); (G.V.); (V.S.)
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3
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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4
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Shiah JV, Johnson DE, Grandis JR. Transcription Factors and Cancer: Approaches to Targeting. Cancer J 2023; 29:38-46. [PMID: 36693157 PMCID: PMC9881838 DOI: 10.1097/ppo.0000000000000639] [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] [Indexed: 01/25/2023]
Abstract
ABSTRACT Cancer is defined by the presence of uncontrollable cell growth, whereby improper proliferative signaling has overcome regulation by cellular mechanisms. Transcription factors are uniquely situated at the helm of signaling, merging extracellular stimuli with intracellular responses. Therefore, this class of proteins plays a pivotal role in coordinating the correct gene expression levels for maintaining normal cellular functions. Dysregulation of transcription factor activity unsurprisingly drives tumorigenesis and oncogenic transformation. Although this imparts considerable therapeutic potential to targeting transcription factors, their lack of enzymatic activity renders intervention challenging and has contributed to a sense that transcription factors are "undruggable." Yet, enduring efforts to elucidate strategies for targeting transcription factors as well as a deeper understanding of their interactions with binding partners have led to advancements that are emerging to counter this narrative. Here, we highlight some of these approaches, focusing primarily on therapeutics that have advanced to the clinic.
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Affiliation(s)
- Jamie V Shiah
- From the Department Otolaryngology-Head and Neck Surgery, University of California at San Francisco, San Francisco, CA
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5
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Burakova E, Vasa SK, Linser R. Characterization of conformational heterogeneity via higher-dimensionality, proton-detected solid-state NMR. JOURNAL OF BIOMOLECULAR NMR 2022; 76:197-212. [PMID: 36149571 PMCID: PMC9712413 DOI: 10.1007/s10858-022-00405-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Site-specific heterogeneity of solid protein samples can be exploited as valuable information to answer biological questions ranging from thermodynamic properties determining fibril formation to protein folding and conformational stability upon stress. In particular, for proteins of increasing molecular weight, however, site-resolved assessment without residue-specific labeling is challenging using established methodology, which tends to rely on carbon-detected 2D correlations. Here we develop purely chemical-shift-based approaches for assessment of relative conformational heterogeneity that allows identification of each residue via four chemical-shift dimensions. High dimensionality diminishes the probability of peak overlap in the presence of multiple, heterogeneously broadened resonances. Utilizing backbone dihedral-angle reconstruction from individual contributions to the peak shape either via suitably adapted prediction routines or direct association with a relational database, the methods may in future studies afford assessment of site-specific heterogeneity of proteins without site-specific labeling.
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Affiliation(s)
- Ekaterina Burakova
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Suresh K Vasa
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany
| | - Rasmus Linser
- Department of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Str. 4a, 44227, Dortmund, Germany.
- Department of Chemistry and Pharmacy, Ludwig-Maximilians-University Munich, Butenandtstr. 5-13, 81377, Munich, Germany.
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6
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Loughrey C, Fitzpatrick P, Orr N, Jurek-Loughrey A. The topology of data: Opportunities for cancer research. Bioinformatics 2021; 37:3091-3098. [PMID: 34320632 PMCID: PMC8504620 DOI: 10.1093/bioinformatics/btab553] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 06/14/2021] [Accepted: 07/28/2021] [Indexed: 01/20/2023] Open
Abstract
Motivation Topological methods have recently emerged as a reliable and interpretable framework for extracting information from high-dimensional data, leading to the creation of a branch of applied mathematics called Topological Data Analysis (TDA). Since then, TDA has been progressively adopted in biomedical research. Biological data collection can result in enormous datasets, comprising thousands of features and spanning diverse datatypes. This presents a barrier to initial data analysis as the fundamental structure of the dataset becomes hidden, obstructing the discovery of important features and patterns. TDA provides a solution to obtain the underlying shape of datasets over continuous resolutions, corresponding to key topological features independent of noise. TDA has the potential to support future developments in healthcare as biomedical datasets rise in complexity and dimensionality. Previous applications extend across the fields of neuroscience, oncology, immunology and medical image analysis. TDA has been used to reveal hidden subgroups of cancer patients, construct organizational maps of brain activity and classify abnormal patterns in medical images. The utility of TDA is broad and to understand where current achievements lie, we have evaluated the present state of TDA in cancer data analysis. Results This article aims to provide an overview of TDA in Cancer Research. A brief introduction to the main concepts of TDA is provided to ensure that the article is accessible to readers who are not familiar with this field. Following this, a focussed literature review on the field is presented, discussing how TDA has been applied across heterogeneous datatypes for cancer research.
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Affiliation(s)
- Ciara Loughrey
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, BT9 5BN, United Kingdom
| | - Padraig Fitzpatrick
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, BT9 5BN, United Kingdom
| | - Nick Orr
- Patrick G Johnston Centre for Cancer Research, Queen's University Belfast, BT9 7AE, United Kingdom
| | - Anna Jurek-Loughrey
- School of Electronics, Electrical Engineering and Computer Science, Queen's University Belfast, BT9 5BN, United Kingdom
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Samarasinghe KTG, Crews CM. Targeted protein degradation: A promise for undruggable proteins. Cell Chem Biol 2021; 28:934-951. [PMID: 34004187 PMCID: PMC8286327 DOI: 10.1016/j.chembiol.2021.04.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/29/2021] [Accepted: 04/20/2021] [Indexed: 02/06/2023]
Abstract
Protein homeostasis, or "proteostasis," is indispensable for a balanced, healthy environment within the cell. However, when natural proteostasis mechanisms are overwhelmed from excessive loads of dysregulated proteins, their accumulation can lead to disease initiation and progression. Recently, the induced degradation of such disease-causing proteins by heterobifunctional molecules, i.e., PROteolysis TArgeting Chimeras (PROTACs), is emerging as a potential therapeutic modality. In the 2 decades since the PROTAC concept was proposed, several additional Targeted Protein Degradation (TPD) strategies have also been explored to target previously undruggable proteins, such as transcription factors. In this review, we discuss the progress and evolution of the TPD field, the breadth of the proteins targeted by PROTACs and the biological effects of their degradation.
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Affiliation(s)
- Kusal T G Samarasinghe
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Craig M Crews
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Department of Chemistry, Yale University, New Haven, CT 06511, USA; Department of Pharmacology, Yale University, New Haven, CT 06511, USA.
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8
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Sriramulu S, Nandy SK, Ganesan H, Banerjee A, Pathak S. In silico analysis and prediction of transcription factors of the proteins interacting with astrocyte elevated gene-1. Comput Biol Chem 2021; 92:107478. [PMID: 33866140 DOI: 10.1016/j.compbiolchem.2021.107478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 02/24/2021] [Accepted: 03/23/2021] [Indexed: 12/24/2022]
Abstract
Multifunctional in nature, the protein Astrocyte Elevated Gene-1 (AEG-1) controls several cancers through protein-protein interactions. Although, specific physiological processes and molecular functions linked with AEG-1 interactors remain unclear. In our present study, we procured the data of AEG-1 interacting proteins and evaluated their biological functions, associated pathways, and interaction networks using bioinformatic tools. A total of 112 proteins experimentally detected to interact with AEG-1 were collected from various public databases. DAVID 6.8 Online tool was utilized to identify the molecular functions, biological processes, cellular components that aid in understanding the physiological function of AEG-1 and its interactors in several cell types. With the help of integrated network analysis of AEG-1 interactors using Cytoscape 3.8.0 software, cross-talk between various proteins, and associated pathways were revealed. Additionally, the Enrichr online tool was used for performing enrichment of transcription factors of AEG-1 interactors' which further revealed a closely associated self-regulated interaction network of a variety of transcription factors that shape the expression of AEG-1 interacting proteins. As a whole, the study calls for better understanding and elucidation of the pathways and biological roles of both AEG-1 and its interactor proteins that might enable their application as biomarkers and therapeutic targets in various diseases in the very near future.
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Affiliation(s)
- Sushmitha Sriramulu
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, 603 103, India
| | - Suman K Nandy
- Department of Histopathology, Tata Medical Centre, Kolkata, 700160, India.
| | - Harsha Ganesan
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, 603 103, India
| | - Antara Banerjee
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, 603 103, India
| | - Surajit Pathak
- Department of Medical Biotechnology, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education (CARE), Chettinad Hospital and Research Institute (CHRI), Kelambakkam, Chennai, 603 103, India.
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Nagarajan H, Vetrivel U. Microsecond scale sampling of Egr-1 conformational landscape to decipher the impact of its disorder regions on structure–function relationship. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1815731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Hemavathy Nagarajan
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India
- Department of Health Research (Govt. of India), National Institute of Traditional Medicine, Indian Council of Medical Research, Belagavi, India
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Chen J, Liu X, Chen J. Targeting Intrinsically Disordered Proteins through Dynamic Interactions. Biomolecules 2020; 10:E743. [PMID: 32403216 PMCID: PMC7277182 DOI: 10.3390/biom10050743] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/04/2020] [Accepted: 05/09/2020] [Indexed: 12/18/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and have attracted significant interest in understanding if and how they may be targeted using small molecules for therapeutic purposes. While most existing studies have focused on extending the traditional structure-centric drug design strategies and emphasized exploring pre-existing structure features of IDPs for specific binding, several examples have also emerged to suggest that small molecules could achieve specificity in binding IDPs and affect their function through dynamic and transient interactions. These dynamic interactions can modulate the disordered conformational ensemble and often lead to modest compaction to shield functionally important interaction sites. Much work remains to be done on further elucidation of the molecular basis of the dynamic small molecule-IDP interaction and determining how it can be exploited for targeting IDPs in practice. These efforts will rely critically on an integrated experimental and computational framework for disordered protein ensemble characterization. In particular, exciting advances have been made in recent years in enhanced sampling techniques, Graphic Processing Unit (GPU)-computing, and protein force field optimization, which have now allowed rigorous physics-based atomistic simulations to generate reliable structure ensembles for nontrivial IDPs of modest sizes. Such de novo atomistic simulations will play crucial roles in exploring the exciting opportunity of targeting IDPs through dynamic interactions.
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Affiliation(s)
- Jianlin Chen
- Department of Hematology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou 318000, Zhejiang, China;
| | - Xiaorong Liu
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
| | - Jianhan Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, USA;
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, USA
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11
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Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Biochemistry 2019; 58:3144-3154. [PMID: 31260268 PMCID: PMC6791285 DOI: 10.1021/acs.biochem.9b00296] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
The c-MYC transcription
factor is a master regulator of cell growth
and proliferation and is an established target for cancer therapy.
This basic helix–loop–helix Zip protein forms a heterodimer
with its obligatory partner MAX, which binds to DNA via the basic
region. Considerable research efforts are focused on targeting the
heterodimerization interface and the interaction of the complex with
DNA. The only available crystal structure is that of a c-MYC:MAX complex
artificially tethered by an engineered disulfide linker and prebound
to DNA. We have carried out a detailed structural analysis of the
apo form of the c-MYC:MAX complex, with no artificial linker, both
in solution using nuclear magnetic resonance (NMR) spectroscopy and
by X-ray crystallography. We have obtained crystal structures in three
different crystal forms, with resolutions between 1.35 and 2.2 Å,
that show extensive helical structure in the basic region. Determination
of the α-helical propensity using NMR chemical shift analysis
shows that the basic region of c-MYC and, to a lesser extent, that
of MAX populate helical conformations. We have also assigned the NMR
spectra of the c-MYC basic helix–loop–helix Zip motif
in the absence of MAX and showed that the basic region has an intrinsic
helical propensity even in the absence of its dimerization partner.
The presence of helical structure in the basic regions in the absence
of DNA suggests that the molecular recognition occurs via a conformational
selection rather than an induced fit. Our work provides both insight
into the mechanism of DNA binding and structural information to aid
in the development of MYC inhibitors.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Fabrice Gorrec
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark D Allen
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
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Rational design using sequence information only produces a peptide that binds to the intrinsically disordered region of p53. Sci Rep 2019; 9:8584. [PMID: 31253862 PMCID: PMC6599006 DOI: 10.1038/s41598-019-44688-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 05/22/2019] [Indexed: 01/19/2023] Open
Abstract
Intrinsically disordered regions (IDRs) of proteins are involved in many diseases. The rational drug design against disease-mediating proteins is often based on the 3D structure; however, the flexible structure of IDRs hinders the use of such structure-based design methods. Here, we developed a rational design method to obtain a peptide that can bind an IDR using only sequence information based on the statistical contact energy of amino acid pairs. We applied the method to the disordered C-terminal domain of the tumor suppressor p53. Titration experiments revealed that one of the designed peptides, DP6, has a druggable affinity of ~1 μM to the p53 C-terminal domain. NMR spectroscopy and molecular dynamics simulation revealed that DP6 selectively binds to the vicinity of the target sequence in the C-terminal domain of p53. DP6 inhibits the nonspecific DNA binding of a tetrameric form of the p53 C-terminal domain, but does not significantly affect the specific DNA binding of a tetrameric form of the p53 core domain. Single-molecule measurements revealed that DP6 retards the 1D sliding of p53 along DNA, implying modulation of the target searching of p53. Statistical potential-based design may be useful in designing peptides that target IDRs for therapeutic purposes.
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13
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Rational modulator design by exploitation of protein-protein complex structures. Future Med Chem 2019; 11:1015-1033. [PMID: 31141413 DOI: 10.4155/fmc-2018-0433] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The horizon of drug discovery is currently expanding to target and modulate protein-protein interactions (PPIs) in globular proteins and intrinsically disordered proteins that are involved in various diseases. To either interrupt or stabilize PPIs, the 3D structure of target protein-protein (or protein-peptide) complexes can be exploited to rationally design PPI modulators (inhibitors or stabilizers) through structure-based molecular design. In this review, we present an overview of experimental and computational methods that can be used to determine 3D structures of protein-protein complexes. Several approaches including rational and in silico methods that can be applied to design peptides, peptidomimetics and small compounds by utilization of determined 3D protein-protein/peptide complexes are summarized and illustrated.
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14
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Martinelli AHS, Lopes FC, John EBO, Carlini CR, Ligabue-Braun R. Modulation of Disordered Proteins with a Focus on Neurodegenerative Diseases and Other Pathologies. Int J Mol Sci 2019; 20:ijms20061322. [PMID: 30875980 PMCID: PMC6471803 DOI: 10.3390/ijms20061322] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/03/2019] [Accepted: 02/12/2019] [Indexed: 12/15/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) do not have rigid 3D structures, showing changes in their folding depending on the environment or ligands. Intrinsically disordered proteins are widely spread in eukaryotic genomes, and these proteins participate in many cell regulatory metabolism processes. Some IDPs, when aberrantly folded, can be the cause of some diseases such as Alzheimer′s, Parkinson′s, and prionic, among others. In these diseases, there are modifications in parts of the protein or in its entirety. A common conformational variation of these IDPs is misfolding and aggregation, forming, for instance, neurotoxic amyloid plaques. In this review, we discuss some IDPs that are involved in neurodegenerative diseases (such as beta amyloid, alpha synuclein, tau, and the “IDP-like” PrP), cancer (p53, c-Myc), and diabetes (amylin), focusing on the structural changes of these IDPs that are linked to such pathologies. We also present the IDP modulation mechanisms that can be explored in new strategies for drug design. Lastly, we show some candidate drugs that can be used in the future for the treatment of diseases caused by misfolded IDPs, considering that cancer therapy has more advanced research in comparison to other diseases, while also discussing recent and future developments in this area of research. Therefore, we aim to provide support to the study of IDPs and their modulation mechanisms as promising approaches to combat such severe diseases.
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Affiliation(s)
- Anne H S Martinelli
- Department of Molecular Biology and Biotechnology & Department of Biophysics, Biosciences Institute-IB, (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Fernanda C Lopes
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Elisa B O John
- Center for Biotechnology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
| | - Célia R Carlini
- Graduate Program in Cell and Molecular Biology, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre CEP 91501-970, RS, Brazil.
- Graduate Program in Medicine and Health Sciences, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 91410-000, RS, Brazil.
- Brain Institute-InsCer, Laboratory of Neurotoxins, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre CEP 90610-000, RS, Brazil.
| | - Rodrigo Ligabue-Braun
- Department of Pharmaceutical Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre CEP 90050-170, RS, Brazil.
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15
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Regulation of fibroblast-like synoviocyte transformation by transcription factors in arthritic diseases. Biochem Pharmacol 2019; 165:145-151. [PMID: 30878552 DOI: 10.1016/j.bcp.2019.03.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2019] [Accepted: 03/12/2019] [Indexed: 02/07/2023]
Abstract
Inflammation in the synovium is known to mediate joint destruction in several forms of arthritis. Fibroblast-like synoviocytes (FLS) are cells that reside in the synovial lining of joints and are known to be key contributors to inflammation associated with arthritis. FLS are a major source of inflammatory cytokines and catabolic enzymes that promote joint degeneration. We now know that there exists a direct correlation between the signaling pathways that are activated by the pro-inflammatory molecules produced by the FLS, and the severity of joint degeneration in arthritis. Research focused on understanding the signaling pathways that are activated by these pro-inflammatory molecules has led to major advancements in the understanding of the joint pathology in arthritis. Transcription factors (TFs) that act as downstream mediators of the pro-inflammatory signaling cascades in various cell types have been reported to play an important role in inducing the deleterious transformation of the FLS. Interestingly, recent studies have started uncovering that several TFs that were previously reported to play role in embryonic development and cancer, but not known to have pronounced roles in tissue inflammation, can actually play crucial roles in the regulation of the pathological properties of the FLS. In this review, we will discuss reports that have been able to impart novel arthritogenic roles to TFs that are specialized in embryonic development. We also discuss the therapeutic potential of targeting these newly identified regulators of FLS transformation in the treatment of arthritis.
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16
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Berlow RB, Martinez-Yamout MA, Dyson HJ, Wright PE. Role of Backbone Dynamics in Modulating the Interactions of Disordered Ligands with the TAZ1 Domain of the CREB-Binding Protein. Biochemistry 2019; 58:1354-1362. [PMID: 30775911 DOI: 10.1021/acs.biochem.8b01290] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The intrinsically disordered transactivation domains of HIF-1α and CITED2 compete for binding of the TAZ1 domain of the CREB-binding protein by a unidirectional allosteric mechanism involving direct competition for shared binding sites, ternary complex formation, and TAZ1 conformational changes. To gain insight into the mechanism by which CITED2 displaces HIF-1α from TAZ1, we used nuclear magnetic resonance spin relaxation methods to obtain an atomic-level description of the picosecond to nanosecond backbone dynamics that contribute to TAZ1 binding and competition. We show that HIF-1α and CITED2 adopt different dynamics in their complexes with TAZ1, with flexibility observed for HIF-1α in regions that would maintain accessibility for CITED2 to bind to TAZ1 and facilitate subsequent HIF-1α dissociation. In contrast, critical regions of CITED2 adopt a rigid structure in its complex with TAZ1, minimizing the ability of HIF-1α to compete for binding. We also find that TAZ1, previously thought to be a rigid scaffold for binding of disordered protein ligands, displays altered backbone dynamics in its various bound states. TAZ1 is more rigid in its CITED2-bound state than in its free state or in complex with HIF-1α, with increased rigidity observed not only in the CITED2 binding site but also in regions of TAZ1 that undergo conformational changes between the HIF-1α- and CITED2-bound structures. Taken together, these data suggest that backbone dynamics in TAZ1, as well as in the HIF-1α and CITED2 ligands, play a role in modulating the occupancy of TAZ1 and highlight the importance of characterizing both binding partners in molecular interactions.
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Affiliation(s)
- Rebecca B Berlow
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Maria A Martinez-Yamout
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - H Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
| | - Peter E Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States
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17
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Lu H, Liu R, Zhou Q. Balanced between order and disorder: a new phase in transcription elongation control and beyond. Transcription 2019; 10:157-163. [PMID: 30663929 DOI: 10.1080/21541264.2019.1570812] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
We recently reported that the cyclin T1 histidine-rich domain creates a phase-separated environment to promote hyperphosphorylation of RNA polymerase II C-terminal domain and robust transcriptional elongation by P-TEFb. Here, we discuss this and several other recent discoveries to demonstrate that phase separation is important for controlling various aspects of transcription.
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Affiliation(s)
- Huasong Lu
- a Department of Molecular and Cell Biology , University of California , Berkeley , CA , USA
| | - Rongdiao Liu
- b School of Pharmaceutical Sciences , Xiamen University , Xiamen , Fujian , China
| | - Qiang Zhou
- a Department of Molecular and Cell Biology , University of California , Berkeley , CA , USA
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18
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Sammak S, Allen MD, Hamdani N, Bycroft M, Zinzalla G. The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex. FEBS J 2018; 285:4165-4180. [PMID: 30222246 PMCID: PMC6398391 DOI: 10.1111/febs.14660] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/14/2018] [Indexed: 12/14/2022]
Abstract
c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the interaction regions on both INI1 and on the c‐MYC:MAX heterodimer. c‐MYC interacts with a highly conserved groove on INI1, while INI1 binds to the c‐MYC helix‐loop‐helix region. The binding site overlaps with the c‐MYC DNA‐binding region, and we show that binding of INI1 and E‐box DNA to c‐MYC:MAX are mutually exclusive.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark D Allen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
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19
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Guca E, Suñol D, Ruiz L, Konkol A, Cordero J, Torner C, Aragon E, Martin-Malpartida P, Riera A, Macias MJ. TGIF1 homeodomain interacts with Smad MH1 domain and represses TGF-β signaling. Nucleic Acids Res 2018; 46:9220-9235. [PMID: 30060237 PMCID: PMC6158717 DOI: 10.1093/nar/gky680] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022] Open
Abstract
TGIF1 is a multifunctional protein that represses TGF-β-activated transcription by interacting with Smad2-Smad4 complexes. We found that the complex structure of TGIF1-HD bound to the TGACA motif revealed a combined binding mode that involves the HD core and the major groove, on the one hand, and the amino-terminal (N-term) arm and the minor groove of the DNA, on the other. We also show that TGIF1-HD interacts with the MH1 domain of Smad proteins, thereby indicating that TGIF1-HD is also a protein-binding domain. Moreover, the formation of the HD-MH1 complex partially hinders the DNA-binding site of the complex, preventing the efficient interaction of TGIF1-HD with DNA. We propose that the binding of the TGIF1 C-term to the Smad2-MH2 domain brings both the HD and MH1 domain into close proximity. This local proximity facilitates the interaction of these DNA-binding domains, thus strengthening the formation of the protein complex versus DNA binding. Once the protein complex has been formed, the TGIF1-Smad system would be released from promoters/enhancers, thereby illustrating one of the mechanisms used by TGIF1 to exert its function as an active repressor of Smad-induced TGF-β signaling.
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Affiliation(s)
- Ewelina Guca
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - David Suñol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Lidia Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Agnieszka Konkol
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Jorge Cordero
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Carles Torner
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Eric Aragon
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Pau Martin-Malpartida
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- Departament de Química Inorgànica i Orgànica, Secció de Química Orgànica, Universitat de Barcelona, Martí i Franquès 1-11, 08028, Barcelona, Spain
| | - Maria J Macias
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, Barcelona 08028, Spain
- ICREA, Passeig Lluís Companys 23, 08010-Barcelona, Spain
- To whom correspondence should be addressed. Tel: +34 934037189;
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20
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Kumar D, Sharma N, Giri R. Therapeutic Interventions of Cancers Using Intrinsically Disordered Proteins as Drug Targets: c-Myc as Model System. Cancer Inform 2017; 16:1176935117699408. [PMID: 28469390 PMCID: PMC5392011 DOI: 10.1177/1176935117699408] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 02/20/2017] [Indexed: 12/29/2022] Open
Abstract
The concept of protein intrinsic disorder has taken the driving seat to understand regulatory proteins in general. Reports suggest that in mammals nearly 75% of signalling proteins contain long disordered regions with greater than 30 amino acid residues. Therefore, intrinsically disordered proteins (IDPs) have been implicated in several human diseases and should be considered as potential novel drug targets. Moreover, intrinsic disorder provides a huge multifunctional capability to hub proteins such as c-Myc and p53. c-Myc is the hot spot for understanding and developing therapeutics against cancers and cancer stem cells. Our past understanding is mainly based on in vitro and in vivo experiments conducted using c-Myc as whole protein. Using the reductionist approach, c-Myc oncoprotein has been divided into structured and disordered domains. A wealth of data is available dealing with the structured perspectives of c-Myc, but understanding c-Myc in terms of disordered domains has just begun. Disorderness provides enormous flexibility to proteins in general for binding to numerous partners. Here, we have reviewed the current progress on understanding c-Myc using the emerging concept of IDPs.
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Affiliation(s)
- Deepak Kumar
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Nitin Sharma
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
| | - Rajanish Giri
- School of Basic Sciences, Indian Institute of Technology Mandi, Mandi, India
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21
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Kong FY, Zhu T, Li N, Cai YF, Zhou K, Wei X, Kou YB, You HJ, Zheng KY, Tang RX. Bioinformatics analysis of the proteins interacting with LASP-1 and their association with HBV-related hepatocellular carcinoma. Sci Rep 2017; 7:44017. [PMID: 28266596 PMCID: PMC5339786 DOI: 10.1038/srep44017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/02/2017] [Indexed: 12/11/2022] Open
Abstract
LIM and SH3 domain protein (LASP-1) is responsible for the development of several types of human cancers via the interaction with other proteins; however, the precise biological functions of proteins interacting with LASP-1 are not fully clarified. Although the role of LASP-1 in hepatocarcinogenesis has been reported, the implication of LASP-1 interactors in HBV-related hepatocellular carcinoma (HCC) is not clearly evaluated. We obtained information regarding LASP-1 interactors from public databases and published studies. Via bioinformatics analysis, we found that LASP-1 interactors were related to distinct molecular functions and associated with various biological processes. Through an integrated network analysis of the interaction and pathways of LASP-1 interactors, cross-talk between different proteins and associated pathways was found. In addition, LASP-1 and several its interactors are significantly altered in HBV-related HCC through microarray analysis and could form a complex co-expression network. In the disease, LASP-1 and its interactors were further predicted to be regulated by a complex interaction network composed of different transcription factors. Besides, numerous LASP-1 interactors were associated with various clinical factors and related to the survival and recurrence of HBV-related HCC. Taken together, these results could help enrich our understanding of LASP-1 interactors and their relationships with HBV-related HCC.
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Affiliation(s)
- Fan-Yun Kong
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ting Zhu
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Nan Li
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yun-Fei Cai
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Kai Zhou
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xiao Wei
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan-Bo Kou
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hong-Juan You
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Kui-Yang Zheng
- Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Ren-Xian Tang
- Jiangsu Key Laboratory of Brain Disease Bioinformation, Xuzhou Medical University, Xuzhou, Jiangsu, China.,Department of Pathogenic Biology and Immunology, Jiangsu Key Laboratory of Immunity and Metabolism, Xuzhou Medical University, Xuzhou, Jiangsu, China
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22
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Shammas SL. Mechanistic roles of protein disorder within transcription. Curr Opin Struct Biol 2017; 42:155-161. [PMID: 28262589 DOI: 10.1016/j.sbi.2017.02.003] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 01/26/2017] [Accepted: 02/13/2017] [Indexed: 12/28/2022]
Abstract
Understanding the interactions of proteins involved in transcriptional regulation is critical to describing biological systems because they control the expression profile of the cell. Yet sadly they belong to a less well biophysically characterized subset of proteins; they frequently contain long disordered regions that are highly dynamic. A key question therefore is, why? What functional roles does protein disorder play in transcriptional regulation? Experimental data exemplifying these roles are starting to emerge, with common themes being enabling complexity within networks and quick responses. Most recently a role for disorder in mediating phase transitions of membrane-less organelles has been proposed.
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Affiliation(s)
- Sarah L Shammas
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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23
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Zeng D, Shen Q, Cho JH. Thermodynamic contribution of backbone conformational entropy in the binding between SH3 domain and proline-rich motif. Biochem Biophys Res Commun 2017; 484:21-26. [DOI: 10.1016/j.bbrc.2017.01.089] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Accepted: 01/18/2017] [Indexed: 01/08/2023]
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24
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Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR. Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angew Chem Int Ed Engl 2017; 56:524-529. [PMID: 27918136 PMCID: PMC5291322 DOI: 10.1002/anie.201609427] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/18/2016] [Indexed: 02/04/2023]
Abstract
There is a lack of current treatment options for ovarian clear cell carcinoma (CCC) and the cancer is often resistant to platinum-based chemotherapy. Hence there is an urgent need for novel therapeutics. The transcription factor hepatocyte nuclear factor 1β (HNF1β) is ubiquitously overexpressed in CCC and is seen as an attractive therapeutic target. This was validated through shRNA-mediated knockdown of the target protein, HNF1β, in five high- and low-HNF1β-expressing CCC lines. To inhibit the protein function, cell-permeable, non-helical constrained proteomimetics to target the HNF1β-importin α protein-protein interaction were designed, guided by X-ray crystallographic data and molecular dynamics simulations. In this way, we developed the first reported series of constrained peptide nuclear import inhibitors. Importantly, this general approach may be extended to other transcription factors.
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Affiliation(s)
- Mareike M. Wiedmann
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
| | - Yuteng Wu
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Shintaro Aibara
- SciLifeLabTomtebodavägen 23A171 65 SolnaStockholmSweden
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - Wenshu Xu
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Hannah F. Sore
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and ResearchA*STAR30 Biopolis Street, #07-01 MatrixSingapore138671Singapore
- School of Biological SciencesNanyang Technological University60 Nanyang DriveSingapore637551Singapore
- Department of Biological SciencesNational University of Singapore14 Science Drive 4Singapore117543Singapore
| | - Laura Itzhaki
- Department of PharmacologyTennis Court RoadCambridgeCB2 1PDUK
| | - Murray Stewart
- MRC Laboratory of Molecular BiologyFrancis Crick Avenue, Cambridge Biomedical CampusCambridgeCB2 0QHUK
| | - James D. Brenton
- Cancer Research UK Cambridge InstituteUniversity of CambridgeLi Ka Shing Centre, Robinson WayCambridgeCB2 0REUK
| | - David R. Spring
- Department of ChemistryUniversity of CambridgeLensfield RoadCambridgeCB2 1EWUK
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25
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Wiedmann MM, Tan YS, Wu Y, Aibara S, Xu W, Sore HF, Verma CS, Itzhaki L, Stewart M, Brenton JD, Spring DR. Development of Cell-Permeable, Non-Helical Constrained Peptides to Target a Key Protein-Protein Interaction in Ovarian Cancer. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201609427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Mareike M. Wiedmann
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
- Cancer Research UK Cambridge Institute; University of Cambridge; Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE UK
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research; A*STAR; 30 Biopolis Street, #07-01 Matrix Singapore 138671 Singapore
| | - Yuteng Wu
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Shintaro Aibara
- SciLifeLab; Tomtebodavägen 23A 171 65 Solna Stockholm Sweden
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - Wenshu Xu
- Department of Pharmacology; Tennis Court Road Cambridge CB2 1PD UK
| | - Hannah F. Sore
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Chandra S. Verma
- Bioinformatics Institute, Agency for Science, Technology and Research; A*STAR; 30 Biopolis Street, #07-01 Matrix Singapore 138671 Singapore
- School of Biological Sciences; Nanyang Technological University; 60 Nanyang Drive Singapore 637551 Singapore
- Department of Biological Sciences; National University of Singapore; 14 Science Drive 4 Singapore 117543 Singapore
| | - Laura Itzhaki
- Department of Pharmacology; Tennis Court Road Cambridge CB2 1PD UK
| | - Murray Stewart
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge Biomedical Campus Cambridge CB2 0QH UK
| | - James D. Brenton
- Cancer Research UK Cambridge Institute; University of Cambridge; Li Ka Shing Centre, Robinson Way Cambridge CB2 0RE UK
| | - David R. Spring
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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Zinzalla G. A New Way Forward in Cancer Drug Discovery: Inhibiting the SWI/SNF Chromatin Remodelling Complex. Chembiochem 2016; 17:677-82. [PMID: 26684344 DOI: 10.1002/cbic.201500565] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Indexed: 12/24/2022]
Abstract
Mutations in subunits of the SWI/SNF chromatin remodelling complex are found in 20 % of human cancers. At face value, this would appear to indicate that this multiprotein complex is a potent tumour suppressor. However, it has recently emerged that some mutations in the SWI/SNF complex can have a gain-of-function effect and that in other tumours, such as pancreatic cancer, leukaemia, and breast cancer, the wild-type complex is used to drive cancer. Thus, paradoxically, this "tumour suppressor" has become an attractive target for developing anticancer agents. The SWI/SNF complex makes several protein-protein interactions both within the complex and with a wide range of transcription factors, and targeting these protein-protein interactions is emerging as the best approach to modulating the activity of the complex selectively.
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Affiliation(s)
- Giovanna Zinzalla
- Microbiology, Tumour and Cell Biology (MTC), and Science for Life Laboratory (SciLifeLab), Karolinska Institutet, Tomtebodavägen 23A, Stockholm, 171 65, Sweden.
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