1
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Iglesias V, Bárcenas O, Pintado-Grima C, Burdukiewicz M, Ventura S. Structural information in therapeutic peptides: Emerging applications in biomedicine. FEBS Open Bio 2024. [PMID: 38877295 DOI: 10.1002/2211-5463.13847] [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: 02/29/2024] [Revised: 05/08/2024] [Accepted: 05/27/2024] [Indexed: 06/16/2024] Open
Abstract
Peptides are attracting a growing interest as therapeutic agents. This trend stems from their cost-effectiveness and reduced immunogenicity, compared to antibodies or recombinant proteins, but also from their ability to dock and interfere with large protein-protein interaction surfaces, and their higher specificity and better biocompatibility relative to organic molecules. Many tools have been developed to understand, predict, and engineer peptide function. However, most state-of-the-art approaches treat peptides only as linear entities and disregard their structural arrangement. Yet, structural details are critical for peptide properties such as solubility, stability, or binding affinities. Recent advances in peptide structure prediction have successfully addressed the scarcity of confidently determined peptide structures. This review will explore different therapeutic and biotechnological applications of peptides and their assemblies, emphasizing the importance of integrating structural information to advance these endeavors effectively.
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Affiliation(s)
- Valentín Iglesias
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Oriol Bárcenas
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Institute of Advanced Chemistry of Catalonia (IQAC), CSIC, Barcelona, Spain
| | - Carlos Pintado-Grima
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Michał Burdukiewicz
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Barcelona, Spain
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2
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Rajiv Gandhi G, Sharanya CS, Jayanandan A, Haridas M, Edwin Hillary V, Rajiv Gandhi S, Sridharan G, Sivasubramanian R, Silva Vasconcelos AB, Montalvão MM, Antony Ceasar S, Sousa NFD, Scotti L, Scotti MT, Gurgel RQ, Quintans-Júnior LJ. Multitargeted molecular docking and dynamics simulation studies of flavonoids and volatile components from the peel of Citrus sinensis L. (Osbeck) against specific tumor protein markers. J Biomol Struct Dyn 2024; 42:3051-3080. [PMID: 37203996 DOI: 10.1080/07391102.2023.2212062] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 05/01/2023] [Indexed: 05/20/2023]
Abstract
Citrus sinensis (L.) Osbeck (Rutaceae), commonly known as the sweet orange, is a popular and widely consumed fruit with several medicinal properties. The present study aimed to perform the in silico screening of 18 flavonoids and eight volatile components from the peel of C. sinensis against apoptotic and inflammatory proteins, metalloprotease, and tumor suppressor markers. Flavonoids obtained higher probabilities than volatile components against selected anti-cancer drug targets. Hence, the data from the binding energies against the essential apoptotic and cell proliferation proteins substantiate that they may be promising compounds in developing effective candidates to block cell growth, proliferation, and induced cell death by activating the apoptotic pathway. Further, the binding stability of the selected targets and the corresponding molecules were analyzed by 100 ns molecular dynamics (MD) simulations. Chlorogenic acid has the most binding affinity against the important anti-cancer targets iNOS, MMP-9, and p53. The congruent binding mode to different drug targets focused on cancer shown by chlorogenic acid suggests that it may be a compound with significant therapeutic potential. Moreover, the binding energy predictions indicated that the compound had stable electrostatic and van der Waal energies. Thus, our data reinforce the medicinal importance of flavonoids from C. sinensis and expand the need for more studies, seeking to optimize results and amplify the impacts of further in vitro and in vivo studies. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gopalsamy Rajiv Gandhi
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Chelankara Suresh Sharanya
- Division of Phytochemistry and Drug Design, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Abhithaj Jayanandan
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Madathilkovilakath Haridas
- Department of Biotechnology and Microbiology, Dr. Janaki Ammal Campus, Kannur University, Thalassery, Kannur, India
| | - Varghese Edwin Hillary
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Sathiyabama Rajiv Gandhi
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Gurunagarajan Sridharan
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Rengaraju Sivasubramanian
- Department of Biochemistry, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirapalli, India
| | - Alan Bruno Silva Vasconcelos
- Postgraduate Program of Physiological Sciences (PROCFIS), Federal University of Sergipe (UFS), São Cristóvão, Sergipe, Brazil
| | - Monalisa Martins Montalvão
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Stanislaus Antony Ceasar
- Division of Plant Molecular Biology and Biotechnology, Department of Biosciences, Rajagiri College of Social Sciences, Kalamassery, Kochi, India
| | - Natália Ferreira de Sousa
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Luciana Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Marcus Tullius Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraíba, Paraíba, Brazil
| | - Ricardo Queiroz Gurgel
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
| | - Lucindo José Quintans-Júnior
- Laboratory of Neuroscience and Pharmacological Assays (LANEF), Department of Physiology (DFS), Federal University of Sergipe, São Cristóvão, Sergipe, Brazil
- Postgraduate Program of Health Sciences (PPGCS), University Hospital, Federal University of Sergipe (HU-UFS), Aracaju, Sergipe, Brazil
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3
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Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [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: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
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Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
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4
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Papadimitropoulou A, Makri M, Zoidis G. MYC the oncogene from hell: Novel opportunities for cancer therapy. Eur J Med Chem 2024; 267:116194. [PMID: 38340508 DOI: 10.1016/j.ejmech.2024.116194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024]
Abstract
Cancer comprises a heterogeneous disease, characterized by diverse features such as constitutive expression of oncogenes and/or downregulation of tumor suppressor genes. MYC constitutes a master transcriptional regulator, involved in many cellular functions and is aberrantly expressed in more than 70 % of human cancers. The Myc protein belongs to a family of transcription factors whose structural pattern is referred to as basic helix-loop-helix-leucine zipper. Myc binds to its partner, a smaller protein called Max, forming an Myc:Max heterodimeric complex that interacts with specific DNA recognition sequences (E-boxes) and regulates the expression of downstream target genes. Myc protein plays a fundamental role for the life of a cell, as it is involved in many physiological functions such as proliferation, growth and development since it controls the expression of a very large percentage of genes (∼15 %). However, despite the strict control of MYC expression in normal cells, MYC is often deregulated in cancer, exhibiting a key role in stimulating oncogenic process affecting features such as aberrant proliferation, differentiation, angiogenesis, genomic instability and oncogenic transformation. In this review we aim to meticulously describe the fundamental role of MYC in tumorigenesis and highlight its importance as an anticancer drug target. We focus mainly on the different categories of novel small molecules that act as inhibitors of Myc function in diverse ways hence offering great opportunities for an efficient cancer therapy. This knowledge will provide significant information for the development of novel Myc inhibitors and assist to the design of treatments that would effectively act against Myc-dependent cancers.
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Affiliation(s)
- Adriana Papadimitropoulou
- Center for Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, 11527, Greece
| | - Maria Makri
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece
| | - Grigoris Zoidis
- Division of Pharmaceutical Chemistry, Department of Pharmacy, School of Health Sciences, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771, Athens, Greece.
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5
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Lama D, Vosselman T, Sahin C, Liaño-Pons J, Cerrato CP, Nilsson L, Teilum K, Lane DP, Landreh M, Arsenian Henriksson M. A druggable conformational switch in the c-MYC transactivation domain. Nat Commun 2024; 15:1865. [PMID: 38424045 PMCID: PMC10904854 DOI: 10.1038/s41467-024-45826-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/06/2024] [Indexed: 03/02/2024] Open
Abstract
The c-MYC oncogene is activated in over 70% of all human cancers. The intrinsic disorder of the c-MYC transcription factor facilitates molecular interactions that regulate numerous biological pathways, but severely limits efforts to target its function for cancer therapy. Here, we use a reductionist strategy to characterize the dynamic and structural heterogeneity of the c-MYC protein. Using probe-based Molecular Dynamics (MD) simulations and machine learning, we identify a conformational switch in the c-MYC amino-terminal transactivation domain (termed coreMYC) that cycles between a closed, inactive, and an open, active conformation. Using the polyphenol epigallocatechin gallate (EGCG) to modulate the conformational landscape of coreMYC, we show through biophysical and cellular assays that the induction of a closed conformation impedes its interactions with the transformation/transcription domain-associated protein (TRRAP) and the TATA-box binding protein (TBP) which are essential for the transcriptional and oncogenic activities of c-MYC. Together, these findings provide insights into structure-activity relationships of c-MYC, which open avenues towards the development of shape-shifting compounds to target c-MYC as well as other disordered transcription factors for cancer treatment.
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Affiliation(s)
- Dilraj Lama
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
| | - Thibault Vosselman
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Cagla Sahin
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - Judit Liaño-Pons
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Carmine P Cerrato
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Lennart Nilsson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14813, Huddinge, Sweden
| | - Kaare Teilum
- Department of Biology, Structural Biology and NMR Laboratory and the Linderstrøm-Lang Centre for Protein Science, University of Copenhagen, DK-2200, Copenhagen, Denmark
| | - David P Lane
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden
| | - Michael Landreh
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Department of Cell- and Molecular Biology, Uppsala University, SE-751 24, Uppsala, Sweden.
| | - Marie Arsenian Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Biomedicum, SE-17165, Stockholm, Sweden.
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund University, SE-221 00, Lund, Sweden.
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6
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Schütz S, Bergsdorf C, Hänni-Holzinger S, Lingel A, Renatus M, Gossert AD, Jahnke W. Intrinsically Disordered Regions in the Transcription Factor MYC:MAX Modulate DNA Binding via Intramolecular Interactions. Biochemistry 2024. [PMID: 38264995 DOI: 10.1021/acs.biochem.3c00608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2024]
Abstract
The basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factor (TF) MYC is in large part an intrinsically disordered oncoprotein. In complex with its obligate heterodimerization partner MAX, MYC preferentially binds E-Box DNA sequences (CANNTG). At promoters containing these sequence motifs, MYC controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. A vast network of proteins in turn regulates MYC function via intermolecular interactions. In this work, we establish another layer of MYC regulation by intramolecular interactions. We used nuclear magnetic resonance (NMR) spectroscopy to identify and map multiple binding sites for the C-terminal MYC:MAX DNA-binding domain (DBD) on the intrinsically disordered regions (IDRs) in the MYC N-terminus. We find that these binding events in trans are driven by electrostatic attraction, that they have distinct affinities, and that they are competitive with DNA binding. Thereby, we observe the strongest effects for the N-terminal MYC box 0 (Mb0), a conserved motif involved in MYC transactivation and target gene induction. We prepared recombinant full-length MYC:MAX complex and demonstrate that the interactions identified in this work are also relevant in cis, i.e., as intramolecular interactions. These findings are supported by surface plasmon resonance (SPR) experiments, which revealed that intramolecular IDR:DBD interactions in MYC decelerate the association of MYC:MAX complexes to DNA. Our work offers new insights into how bHLH-LZ TFs are regulated by intramolecular interactions, which open up new possibilities for drug discovery.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Sandra Hänni-Holzinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | | | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
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7
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Li L, Zhang D, Cao X. EBF1, PAX5, and MYC: regulation on B cell development and association with hematologic neoplasms. Front Immunol 2024; 15:1320689. [PMID: 38318177 PMCID: PMC10839018 DOI: 10.3389/fimmu.2024.1320689] [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: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
During lymphocyte development, a diverse repertoire of lymphocyte antigen receptors is produced to battle against pathogens, which is the basis of adaptive immunity. The diversity of the lymphocyte antigen receptors arises primarily from recombination-activated gene (RAG) protein-mediated V(D)J rearrangement in early lymphocytes. Furthermore, transcription factors (TFs), such as early B cell factor 1 (EBF1), paired box gene 5 (PAX5), and proto-oncogene myelocytomatosis oncogene (MYC), play critical roles in regulating recombination and maintaining normal B cell development. Therefore, the aberrant expression of these TFs may lead to hematologic neoplasms.
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Affiliation(s)
- Li Li
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
| | - Daiquan Zhang
- Department of Traditional Chinese Medicine, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Xinmei Cao
- Immune Mechanism and Therapy of Major Diseases of Luzhou Key Laboratory, School of Basic Medical Sciences, Southwest Medical University, Luzhou, China
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8
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Gunasinghe KJ, Rahman T, Chee Wezen X. Unraveling the Behavior of Intrinsically Disordered Protein c-Myc: A Study Utilizing Gaussian-Accelerated Molecular Dynamics. ACS OMEGA 2024; 9:2250-2262. [PMID: 38250404 PMCID: PMC10795134 DOI: 10.1021/acsomega.3c05822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/02/2023] [Accepted: 11/21/2023] [Indexed: 01/23/2024]
Abstract
The protein c-Myc is a transcription factor that remains largely intrinsically disordered and is known to be involved in various biological processes and is overexpressed in various cancers, making it an attractive drug target. However, intrinsically disordered proteins such as c-Myc do not show funnel-like basins in their free-energy landscapes; this makes their druggability a challenge. For the first time, we propose a heterodimer model of c-Myc/Max in full length in this work. We used Gaussian-accelerated molecular dynamics (GaMD) simulations to explore the behavior of c-Myc and its various regions, including the transactivation domain (TAD) and the basic helix-loop-helix-leucine-zipper (bHLH-Zipper) motif in three different conformational states: (a) monomeric c-Myc, (b) c-Myc when bound to its partner protein, Max, and (c) when Max was removed after binding. We analyzed the GaMD trajectories using root-mean-square deviation (RMSD), radius of gyration, root-mean-square fluctuation, and free-energy landscape (FEL) calculations to elaborate the behaviors of these regions. The results showed that the monomeric c-Myc structure showed a higher RMSD fluctuation as compared with the c-Myc/Max heterodimer in the bHLH-Zipper motif. This indicated that the bHLH-Zipper motif of c-Myc is more stable when it is bound to Max. The TAD region in both monomeric and Max-bound states showed similar plasticity in terms of RMSD. We also conducted residue decomposition calculations and showed that the c-Myc and Max interaction could be driven mainly by electrostatic interactions and the residues Arg299, Ile403, and Leu420 seemed to play important roles in the interaction. Our work provides insights into the behavior of c-Myc and its regions that could support the development of drugs that target c-Myc and other intrinsically disordered proteins.
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Affiliation(s)
| | - Taufiq Rahman
- Department
of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
| | - Xavier Chee Wezen
- Faculty
of Engineering, Computing and Science, Swinburne
University of Technology Sarawak, Kuching 93350, Malaysia
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9
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Harris EL, Roy V, Montagne M, Rose AMS, Livesey H, Reijnders MRF, Hobson E, Sansbury FH, Willemsen MH, Pfundt R, Warren D, Long V, Carr IM, Brunner HG, Sheridan EG, Firth HV, Lavigne P, Poulter JA. A recurrent de novo MAX p.Arg60Gln variant causes a syndromic overgrowth disorder through differential expression of c-Myc target genes. Am J Hum Genet 2024; 111:119-132. [PMID: 38141607 PMCID: PMC10806738 DOI: 10.1016/j.ajhg.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/25/2023] Open
Abstract
Cyclin D2 (CCND2) stabilization underpins a range of macrocephaly-associated disorders through mutation of CCND2 or activating mutations in upstream genes encoding PI3K-AKT pathway components. Here, we describe three individuals with overlapping macrocephaly-associated phenotypes who carry the same recurrent de novo c.179G>A (p.Arg60Gln) variant in Myc-associated factor X (MAX). The mutation, located in the b-HLH-LZ domain, causes increased intracellular CCND2 through increased transcription but it does not cause stabilization of CCND2. We show that the purified b-HLH-LZ domain of MAXArg60Gln (Max∗Arg60Gln) binds its target E-box sequence with a lower apparent affinity. This leads to a more efficient heterodimerization with c-Myc resulting in an increase in transcriptional activity of c-Myc in individuals carrying this mutation. The recent development of Omomyc-CPP, a cell-penetrating b-HLH-LZ-domain c-Myc inhibitor, provides a possible therapeutic option for MAXArg60Gln individuals, and others carrying similar germline mutations resulting in dysregulated transcriptional c-Myc activity.
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Affiliation(s)
- Erica L Harris
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Vincent Roy
- Département de Biochimie et Génomique Fonctionnelle, PROTÉO et Institut de Pharmacologie de Sherbrooke. University of Sherbrooke, Sherbrooke, QC, Canada
| | - Martin Montagne
- Département de Biochimie et Génomique Fonctionnelle, PROTÉO et Institut de Pharmacologie de Sherbrooke. University of Sherbrooke, Sherbrooke, QC, Canada
| | - Ailsa M S Rose
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Helen Livesey
- Leeds Teaching Hospitals NHS Trust, Leeds, UK; All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Cardiff, UK
| | - Margot R F Reijnders
- Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Emma Hobson
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Cardiff, UK
| | - Marjolein H Willemsen
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | | | - Vernon Long
- Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Ian M Carr
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Han G Brunner
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Eamonn G Sheridan
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK; Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Helen V Firth
- Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Pierre Lavigne
- Département de Biochimie et Génomique Fonctionnelle, PROTÉO et Institut de Pharmacologie de Sherbrooke. University of Sherbrooke, Sherbrooke, QC, Canada.
| | - James A Poulter
- Division of Molecular Medicine, Leeds Institute of Medical Research, University of Leeds, Leeds, UK.
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10
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Epasto LM, Pötzl C, Peterlik H, Khalil M, Saint‐Pierre C, Gasparutto D, Sicoli G, Kurzbach D. NMR-identification of the interaction between BRCA1 and the intrinsically disordered monomer of the Myc-associated factor X. Protein Sci 2024; 33:e4849. [PMID: 38037490 PMCID: PMC10731500 DOI: 10.1002/pro.4849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/17/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
The breast cancer susceptibility 1 (BRCA1) protein plays a pivotal role in modulating the transcriptional activity of the vital intrinsically disordered transcription factor MYC. In this regard, mutations of BRCA1 and interruption of its regulatory activity are related to hereditary breast and ovarian cancer (HBOC). Interestingly, so far, MYC's main dimerization partner MAX (MYC-associated factor X) has not been found to bind BRCA1 despite a high sequence similarity between both oncoproteins. Herein, we show that a potential reason for this discrepancy is the heterogeneous conformational space of MAX, which encloses a well-documented folded coiled-coil homodimer as well as a less common intrinsically disordered monomer state-contrary to MYC, which exists mostly as intrinsically disordered protein in the absence of any binding partner. We show that when the intrinsically disordered state of MAX is artificially overpopulated, the binding of MAX to BRCA1 can readily be observed. We characterize this interaction by nuclear magnetic resonance (NMR) spectroscopy chemical shift and relaxation measurements, complemented with ITC and SAXS data. Our results suggest that BRCA1 directly binds the MAX monomer to form a disordered complex. Though probed herein under biomimetic in-vitro conditions, this finding can potentially stimulate new perspectives on the regulatory network around BRCA1 and its involvement in MYC:MAX regulation.
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Affiliation(s)
- Ludovica Martina Epasto
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
| | - Christopher Pötzl
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
| | | | - Mahdi Khalil
- CNRS UMR 8516, LASIREUniversity of LilleVilleneuve d'Ascq CedexFrance
| | | | | | - Giuseppe Sicoli
- CNRS UMR 8516, LASIREUniversity of LilleVilleneuve d'Ascq CedexFrance
| | - Dennis Kurzbach
- Faculty of Chemistry, Institute for Biological ChemistryUniversity of ViennaViennaAustria
- Vienna Doctoral School in Chemistry (DoSChem)University of ViennaViennaAustria
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11
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Bhowmick S, Roy K, Saha A. Structure-guided screening of protein-protein interaction for the identification of Myc-Max heterodimer complex modulators. J Biomol Struct Dyn 2023:1-19. [PMID: 38109131 DOI: 10.1080/07391102.2023.2294174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 12/01/2023] [Indexed: 12/19/2023]
Abstract
De-regulation of oncogenic myelocytomatosis (c-Myc or Myc) transcription factor is one of the most common molecular anomalies encountered in human cancers, and it is typically linked to many aggressive malignancies including breast, lung, cervix, colon glioblastomas, and other haematological organs. The Myc belongs to the basic helix-loop-helix zipper protein family (bHLH-ZIP), and its dimerization with another principal interactor protein partner Myc-associated factor X (Max) is essentially required for cellular transformation, cell growth and proliferation, and transcriptional activation. Intermolecular interactions have been evaluated between hetero-dimer Myc-Max protein, which identified protein-protein interaction (PPI) specific modulators using highly précised molecular docking study followed by long-range interaction stability analyzed through molecular dynamic (MD) simulation. Moreover, ADME profile analyses have been estimated for screened hit compounds. MM-GBSA-based binding free energy (ΔG) estimations have been performed for all screened hit compounds obtained from multi-step molecular docking-based virtual screening technique. According to the employed various rigorous multi-chemometric techniques, four identified inhibitors/modulators appear to have a considerable number of intermolecular contacts with hotspot residues in the hetero-dimer interface region of the Myc-Max PPI complex. However, identified hit compounds might need further structural optimization or extensive biophysical analyses for better understanding of the molecular mechanism for exhibiting the Myc-Max PPI interface binding stability.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - Kunal Roy
- Drug Theoretics and Cheminformatics Laboratory, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | - Achintya Saha
- Department of Chemical Technology, University of Calcutta, Kolkata, India
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12
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GHORBANI ROGHAYEH, GHARBAVI MAHMOUD, SHARAFI ALI, RISMANI ELHAM, REZAEEJAM HAMED, MORTAZAVI YOUSEF, JOHARI BEHROOZ. Targeted anti-tumor synergistic effects of Myc decoy oligodeoxynucleotides-loaded selenium nanostructure combined with chemoradiotherapy on LNCaP prostate cancer cells. Oncol Res 2023; 32:101-125. [PMID: 38188680 PMCID: PMC10767241 DOI: 10.32604/or.2023.044741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 09/13/2023] [Indexed: 01/09/2024] Open
Abstract
In the present study, we investigated the synergistic effects of targeted methotrexate-selenium nanostructure containing Myc decoy oligodeoxynucleotides along with X-irradiation exposure as a combination therapy on LNCaP prostate cancer cells. Myc decoy ODNs were designed based on the promoter of Bcl-2 gene and analyzed by molecular docking and molecular dynamics assays. ODNs were loaded on the synthesized Se@BSA@Chi-MTX nanostructure. The physicochemical characteristics of nanostructures were determined by FTIR, DLS, UV-vis, TEM, EDX, in vitro release, and hemolysis tests. Subsequently, the cytotoxicity properties of them with and without X-irradiation were investigated by uptake, MTT, cell cycle, apoptosis, and scratch assays on the LNCaP cell line. The results of DLS and TEM showed negative charge (-9 mV) and nanometer size (40 nm) for Se@BSA@Chi-DEC-MTX NPs, respectively. The results of FTIR, UV-vis, and EDX showed the proper interaction of different parts and the correct synthesis of nanoparticles. The results of hemolysis showed the hemocompatibility of this nanoparticle in concentrations less than 6 mg/mL. The ODNs release from the nanostructures showed a pH-dependent manner, and the release rate was 15% higher in acidic pH. The targeted Se@BSA@Chi-labeled ODN-MTX NPs were efficiently taken up by LNCaP cells by targeting the prostate-specific membrane antigen (PSMA). The significant synergistic effects of nanostructure (containing MTX drug) treatment along with X-irradiation showed cell growth inhibition, apoptosis induction (~57%), cell cycle arrest (G2/M phase), and migration inhibition (up to 90%) compared to the control. The results suggested that the Se@BSA@Chi-DEC-MTX NPs can potentially suppress the cell growth of LNCaP cells. This nanostructure system can be a promising approach for targeted drug delivery and chemoradiotherapy in prostate cancer treatment.
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Affiliation(s)
- ROGHAYEH GHORBANI
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - MAHMOUD GHARBAVI
- Nanotechnology Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - ALI SHARAFI
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Zanjan University of Medical Sciences, Zanjan, Iran
| | - ELHAM RISMANI
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Pasteur Avenue, Tehran, Iran
| | - HAMED REZAEEJAM
- Department of Radiology Technology, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - YOUSEF MORTAZAVI
- Department of Medical Biotechnology, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
| | - BEHROOZ JOHARI
- Zanjan Pharmaceutical Biotechnology Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
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13
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Liu F, Liao Z, Zhang Z. MYC in liver cancer: mechanisms and targeted therapy opportunities. Oncogene 2023; 42:3303-3318. [PMID: 37833558 DOI: 10.1038/s41388-023-02861-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/28/2023] [Accepted: 10/03/2023] [Indexed: 10/15/2023]
Abstract
MYC, a major oncogenic transcription factor, regulates target genes involved in various pathways such as cell proliferation, metabolism and immune evasion, playing a critical role in the tumor initiation and development in multiple types of cancer. In liver cancer, MYC and its signaling pathways undergo significant changes, exerting a profound impact on liver cancer progression, including tumor proliferation, metastasis, dedifferentiation, metabolism, immune microenvironment, and resistance to comprehensive therapies. This makes MYC an appealing target, despite it being previously considered an undruggable protein. In this review, we discuss the role and mechanisms of MYC in liver physiology, chronic liver diseases, hepatocarcinogenesis, and liver cancer progression, providing a theoretical basis for targeting MYC as an ideal therapeutic target for liver cancer. We also summarize and prospect the strategies for targeting MYC, including direct and indirect approaches to abolish the oncogenic function of MYC in liver cancer.
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Affiliation(s)
- Furong Liu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhibin Liao
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China
| | - Zhanguo Zhang
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, 430030, China.
- Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Wuhan, Hubei, 430030, China.
- Key Laboratory of Organ Transplantation, Ministry of Education; NHC Key Laboratory of Organ Transplantation; Key Laboratory of Organ Transplantation, Chinese Academy of Medical Sciences, Wuhan, China.
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14
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Liu W, Chen L, Yin D, Yang Z, Feng J, Sun Q, Lai L, Guo X. Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins. Nat Commun 2023; 14:5203. [PMID: 37626077 PMCID: PMC10457384 DOI: 10.1038/s41467-023-41018-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023] Open
Abstract
Intrinsically disordered proteins (IDPs) play crucial roles in cellular processes and hold promise as drug targets. However, the dynamic nature of IDPs remains poorly understood. Here, we construct a single-molecule electrical nanocircuit based on silicon nanowire field-effect transistors (SiNW-FETs) and functionalize it with an individual disordered c-Myc bHLH-LZ domain to enable label-free, in situ, and long-term measurements at the single-molecule level. We use the device to study c-Myc interaction with Max and/or small molecule inhibitors. We observe the self-folding/unfolding process of c-Myc and reveal its interaction mechanism with Max and inhibitors through ultrasensitive real-time monitoring. We capture a relatively stable encounter intermediate ensemble of c-Myc during its transition from the unbound state to the fully folded state. The c-Myc/Max and c-Myc/inhibitor dissociation constants derived are consistent with other ensemble experiments. These proof-of-concept results provide an understanding of the IDP-binding/folding mechanism and represent a promising nanotechnology for IDP conformation/interaction studies and drug discovery.
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Affiliation(s)
- Wenzhe Liu
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Limin Chen
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, P. R. China
| | - Dongbao Yin
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Zhiheng Yang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Jianfei Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China
| | - Qi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
| | - Luhua Lai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
- Peking-Tsinghua Center for Life Sciences, Peking University, 100871, Beijing, P. R. China.
- Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, 100871, Beijing, P. R. China.
| | - Xuefeng Guo
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, 292 Chengfu Road, Haidian District, 100871, Beijing, P. R. China.
- Center of Single-Molecule Sciences, Institute of Modern Optics, Frontiers Science Center for New Organic Matter, College of Electronic Information and Optical Engineering, Nankai University, 38 Tongyan Road, Jinnan District, 300350, Tianjin, P. R. China.
- National Biomedical Imaging Center, Peking University, Beijing, 100871, P. R. China.
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Illi B, Nasi S. Myc beyond Cancer: Regulation of Mammalian Tissue Regeneration. PATHOPHYSIOLOGY 2023; 30:346-365. [PMID: 37606389 PMCID: PMC10443299 DOI: 10.3390/pathophysiology30030027] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 07/28/2023] [Accepted: 07/31/2023] [Indexed: 08/23/2023] Open
Abstract
Myc is one of the most well-known oncogenes driving tumorigenesis in a wide variety of tissues. From the brain to blood, its deregulation derails physiological pathways that grant the correct functioning of the cell. Its action is carried out at the gene expression level, where Myc governs basically every aspect of transcription. Indeed, in addition to its role as a canonical, chromatin-bound transcription factor, Myc rules RNA polymerase II (RNAPII) transcriptional pause-release, elongation and termination and mRNA capping. For this reason, it is evident that minimal perturbations of Myc function mirror malignant cell behavior and, consistently, a large body of literature mainly focuses on Myc malfunctioning. In healthy cells, Myc controls molecular mechanisms involved in pivotal functions, such as cell cycle (and proliferation thereof), apoptosis, metabolism and cell size, angiogenesis, differentiation and stem cell self-renewal. In this latter regard, Myc has been found to also regulate tissue regeneration, a hot topic in the research fields of aging and regenerative medicine. Indeed, Myc appears to have a role in wound healing, in peripheral nerves and in liver, pancreas and even heart recovery. Herein, we discuss the state of the art of Myc's role in tissue regeneration, giving an overview of its potent action beyond cancer.
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Affiliation(s)
- Barbara Illi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
| | - Sergio Nasi
- Institute of Molecular Biology and Pathology, National Research Council, c/o Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy
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16
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Zhou M, Boulos JC, Omer EA, Klauck SM, Efferth T. Modes of Action of a Novel c-MYC Inhibiting 1,2,4-Oxadiazole Derivative in Leukemia and Breast Cancer Cells. Molecules 2023; 28:5658. [PMID: 37570631 PMCID: PMC10419799 DOI: 10.3390/molecules28155658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/19/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
The c-MYC oncogene regulates multiple cellular activities and is a potent driver of many highly aggressive human cancers, such as leukemia and triple-negative breast cancer. The oxadiazole class of compounds has gained increasing interest for its anticancer activities. The aim of this study was to investigate the molecular modes of action of a 1,2,4-oxadiazole derivative (ZINC15675948) as a c-MYC inhibitor. ZINC15675948 displayed profound cytotoxicity at the nanomolar range in CCRF-CEM leukemia and MDA-MB-231-pcDNA3 breast cancer cells. Multidrug-resistant sublines thereof (i.e., CEM/ADR5000 and MDA-MB-231-BCRP) were moderately cross-resistant to this compound (<10-fold). Molecular docking and microscale thermophoresis revealed a strong binding of ZINC15675948 to c-MYC by interacting close to the c-MYC/MAX interface. A c-MYC reporter assay demonstrated that ZINC15675948 inhibited c-MYC activity. Western blotting and qRT-PCR showed that c-MYC expression was downregulated by ZINC15675948. Applying microarray hybridization and signaling pathway analyses, ZINC15675948 affected signaling routes downstream of c-MYC in both leukemia and breast cancer cells as demonstrated by the induction of DNA damage using single cell gel electrophoresis (alkaline comet assay) and induction of apoptosis using flow cytometry. ZINC15675948 also caused G2/M phase and S phase arrest in CCRF-CEM cells and MDA-MB-231-pcDNA3 cells, respectively, accompanied by the downregulation of CDK1 and p-CDK2 expression using western blotting. Autophagy induction was observed in CCRF-CEM cells but not MDA-MB-231-pcDNA3 cells. Furthermore, microarray-based mRNA expression profiling indicated that ZINC15675948 may target c-MYC-regulated ubiquitination, since the novel ubiquitin ligase (ELL2) was upregulated in the absence of c-MYC expression. We propose that ZINC15675948 is a promising natural product-derived compound targeting c-MYC in c-MYC-driven cancers through DNA damage, cell cycle arrest, and apoptosis.
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Affiliation(s)
- Min Zhou
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Joelle C. Boulos
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Ejlal A. Omer
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Sabine M. Klauck
- Division of Cancer Genome Research, German Cancer Research Center (DKFZ), German Cancer Consortium (DKTK), National Center for Tumor Disease (NCT), Im Neuenheimer Feld 460, 69120 Heidelberg, Germany
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University-Mainz, Staudinger Weg 5, 55128 Mainz, Germany
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Oei V, Chuang LSH, Matsuo J, Srivastava S, Teh M, Ito Y. RUNX3 inactivates oncogenic MYC through disruption of MYC/MAX complex and subsequent recruitment of GSK3β-FBXW7 cascade. Commun Biol 2023; 6:689. [PMID: 37400551 DOI: 10.1038/s42003-023-05037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/12/2023] [Indexed: 07/05/2023] Open
Abstract
MYC is one of the most commonly dysregulated proto-oncogenes in cancer. MYC promotes cancer initiation and maintenance by regulating multiple biological processes, such as proliferation and stem cell function. Here, we show that developmental regulator RUNX3 targets MYC protein for rapid degradation through the glycogen synthase kinase-3 beta-F-box/WD repeat-containing protein 7 (GSK3β-FBXW7) proteolytic pathway. The evolutionarily conserved Runt domain of RUNX3 interacts directly with the basic helix-loop-helix leucine zipper of MYC, resulting in the disruption of MYC/MAX and MYC/MIZ-1 interactions, enhanced GSK3β-mediated phosphorylation of MYC protein at threonine-58 and its subsequent degradation via the ubiquitin-proteasomal pathway. We therefore uncover a previously unknown mode of MYC destabilization by RUNX3 and provide an explanation as to why RUNX3 inhibits early-stage cancer development in gastrointestinal and lung mouse cancer models.
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Affiliation(s)
- Vincent Oei
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
- NUS Graduate School, Integrative Sciences and Engineering Programme, Singapore, Singapore
| | - Linda Shyue Huey Chuang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Junichi Matsuo
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Supriya Srivastava
- Department of Medicine, National University of Singapore, Singapore, Singapore
| | - Ming Teh
- Department of Pathology, National University of Singapore, Singapore, Singapore
| | - Yoshiaki Ito
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.
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18
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Lu Y, Yang Y, Zhu G, Zeng H, Fan Y, Guo F, Xu D, Wang B, Chen D, Ge G. Emerging Pharmacotherapeutic Strategies to Overcome Undruggable Proteins in Cancer. Int J Biol Sci 2023; 19:3360-3382. [PMID: 37496997 PMCID: PMC10367563 DOI: 10.7150/ijbs.83026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 06/13/2023] [Indexed: 07/28/2023] Open
Abstract
Targeted therapies in cancer treatment can improve in vivo efficacy and reduce adverse effects by altering the tissue exposure of specific biomolecules. However, there are still large number of target proteins in cancer are still undruggable, owing to the following factors including (1) lack of ligand-binding pockets, (2) function based on protein-protein interactions (PPIs), (3) the highly specific conserved active sites among protein family members, and (4) the variability of tertiary docking structures. The current status of undruggable targets proteins such as KRAS, TP53, C-MYC, PTP, are carefully introduced in this review. Some novel techniques and drug designing strategies have been applicated for overcoming these undruggable proteins, and the most classic and well-known technology is proteolysis targeting chimeras (PROTACs). In this review, the novel drug development strategies including targeting protein degradation, targeting PPI, targeting intrinsically disordered regions, as well as targeting protein-DNA binding are described, and we also discuss the potential of these strategies for overcoming the undruggable targets. Besides, intelligence-assisted technologies like Alpha-Fold help us a lot to predict the protein structure, which is beneficial for drug development. The discovery of new targets and the development of drugs targeting them, especially those undruggable targets, remain a huge challenge. New drug development strategies, better extraction processes that do not disrupt protein-protein interactions, and more precise artificial intelligence technologies may provide significant assistance in overcoming these undruggable targets.
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Affiliation(s)
- Yuqing Lu
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Yuewen Yang
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Guanghao Zhu
- Shanghai University of Traditional Chinese Medicine, 201203 Shanghai City, China
| | - Hairong Zeng
- Shanghai University of Traditional Chinese Medicine, 201203 Shanghai City, China
| | - Yiming Fan
- Dalian Harmony Medical Testing Laboratory Co., Ltd, 116620 Dalian City, Liaoning Province, China
| | - Fujia Guo
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Dongshu Xu
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Boya Wang
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Dapeng Chen
- Dalian Medical University, 116044 Dalian City, Liaoning Province, China
| | - Guangbo Ge
- Shanghai University of Traditional Chinese Medicine, 201203 Shanghai City, China
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19
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Karadkhelkar NM, Lin M, Eubanks LM, Janda KD. Demystifying the Druggability of the MYC Family of Oncogenes. J Am Chem Soc 2023; 145:3259-3269. [PMID: 36734615 PMCID: PMC10182829 DOI: 10.1021/jacs.2c12732] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The MYC family of oncogenes (MYC, MYCN, and MYCL) encodes a basic helix-loop-helix leucine zipper (bHLHLZ) transcriptional regulator that is responsible for moving the cell through the restriction point. Through the HLHZIP domain, MYC heterodimerizes with the bHLHLZ protein MAX, which enables this MYC-MAX complex to bind to E-box regulatory DNA elements thereby controlling transcription of a large group of genes and their proteins. Translationally, MYC is one of the foremost oncogenic targets, and deregulation of expression of the MYC family gene/proteins occurs in over half of all human tumors and is recognized as a hallmark of cancer initiation and maintenance. Additionally, unexpected roles for this oncoprotein have been found in cancers that nominally have a non-MYC etiology. Although MYC is rarely mutated, its gain of function in cancer results from overexpression or from amplification. Moreover, MYC is a pleiotropic transcription factor possessing broad pathogenic prominence making it a coveted cancer target. A widely held notion within the biomedical research community is that the reliable modulation of MYC represents a tremendous therapeutic opportunity given its role in directly potentiating oncogenesis. However, the MYC-MAX heterodimer interaction contains a large surface area with a lack of well-defined binding sites creating the perception that targeting of MYC-MAX is forbidding. Here, we discuss the biochemistry behind MYC and MYC-MAX as it relates to cancer progression associated with these transcription factors. We also discuss the notion that MYC should no longer be regarded as undruggable, providing examples that a therapeutic window is achievable despite global MYC inhibition.
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Affiliation(s)
- Nishant M. Karadkhelkar
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Mingliang Lin
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Lisa M. Eubanks
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
| | - Kim D. Janda
- Departments of Chemistry and Immunology, The Skaggs Institute for Chemical Biology, Worm Institute of Research and Medicine (WIRM), The Scripps Research Institute, La Jolla, California 92037, United States
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20
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Portability of a Small-Molecule Binding Site between Disordered Proteins. Biomolecules 2022; 12:biom12121887. [PMID: 36551315 PMCID: PMC9775153 DOI: 10.3390/biom12121887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/07/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) are important in both normal and disease states. Small molecules can be targeted to disordered regions, but we currently have only a limited understanding of the nature of small-molecule binding sites in IDPs. Here, we show that a minimal small-molecule binding sequence of eight contiguous residues derived from the Myc protein can be ported into a different disordered protein and recapitulate small-molecule binding activity in the new context. We also find that the residue immediately flanking the binding site can have opposing effects on small-molecule binding in the different disordered protein contexts. The results demonstrate that small-molecule binding sites can act modularly and are portable between disordered protein contexts but that residues outside of the minimal binding site can modulate binding affinity.
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21
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Schütz S, Bergsdorf C, Goretzki B, Lingel A, Renatus M, Gossert AD, Jahnke W. The disordered MAX N-terminus modulates DNA binding of the transcription factor MYC:MAX. J Mol Biol 2022; 434:167833. [PMID: 36174765 DOI: 10.1016/j.jmb.2022.167833] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 09/05/2022] [Accepted: 09/17/2022] [Indexed: 11/15/2022]
Abstract
The intrinsically disordered protein MYC belongs to the family of basic helix-loop-helix leucine zipper (bHLH-LZ) transcription factors (TFs). In complex with its cognate binding partner MAX, MYC preferentially binds to E-Box promotor sequences where it controls fundamental cellular processes such as cell cycle progression, metabolism, and apoptosis. Intramolecular regulation of MYC:MAX has not yet been investigated in detail. In this work, we use Nuclear Magnetic Resonance (NMR) spectroscopy to identify and map interactions between the disordered MAX N-terminus and the MYC:MAX DNA binding domain (DBD). We find that this binding event is mainly driven by electrostatic interactions and that it is competitive with DNA binding. Using Nuclear Magnetic resonance (NMR) spectroscopy and Surface Plasmon Resonance (SPR), we demonstrate that the MAX N-terminus serves to accelerate DNA binding kinetics of MYC:MAX and MAX:MAX dimers, while it simultaneously provides specificity for E-Box DNA. We also establish that these effects are further enhanced by Casein Kinase 2-mediated phosphorylation of two serine residues in the MAX N-terminus. Our work provides new insights how bHLH-LZ TFs are regulated by intramolecular interactions between disordered regions and the folded DNA binding domain.
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Affiliation(s)
- Stefan Schütz
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christian Bergsdorf
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Benedikt Goretzki
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Andreas Lingel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Alvar D Gossert
- Department of Biology, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Wolfgang Jahnke
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland.
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22
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Jubeen F, Ijaz S, Jabeen I, Aftab U, Mehdi W, Altaf A, Alissa SA, Al-Ghulikah HA, Ezzine S, Bejaoui I, Iqbal M. Anticancer potential of novel 5-Fluorouracil co-crystals against MCF7 breast and SW480 colon cancer cell lines along with docking studies. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.104299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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23
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Bartolucci D, Pession A, Hrelia P, Tonelli R. Precision Anti-Cancer Medicines by Oligonucleotide Therapeutics in Clinical Research Targeting Undruggable Proteins and Non-Coding RNAs. Pharmaceutics 2022; 14:pharmaceutics14071453. [PMID: 35890348 PMCID: PMC9315662 DOI: 10.3390/pharmaceutics14071453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/24/2022] [Accepted: 07/08/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer incidence and mortality continue to increase, while the conventional chemotherapeutic drugs confer limited efficacy and relevant toxic side effects. Novel strategies are urgently needed for more effective and safe therapeutics in oncology. However, a large number of proteins are considered undruggable by conventional drugs, such as the small molecules. Moreover, the mRNA itself retains oncological functions, and its targeting offers the double advantage of blocking the tumorigenic activities of the mRNA and the translation into protein. Finally, a large family of non-coding RNAs (ncRNAs) has recently emerged that are also dysregulated in cancer, but they could not be targeted by drugs directed against the proteins. In this context, this review describes how the oligonucleotide therapeutics targeting RNA or DNA sequences, are emerging as a new class of drugs, able to tackle the limitations described above. Numerous clinical trials are evaluating oligonucleotides for tumor treatment, and in the next few years some of them are expected to reach the market. We describe the oligonucleotide therapeutics targeting undruggable proteins (focusing on the most relevant, such as those originating from the MYC and RAS gene families), and for ncRNAs, in particular on those that are under clinical trial evaluation in oncology. We highlight the challenges and solutions for the clinical success of oligonucleotide therapeutics, with particular emphasis on the peculiar challenges that render it arduous to treat tumors, such as heterogeneity and the high mutation rate. In the review are presented these and other advantages offered by the oligonucleotide as an emerging class of biotherapeutics for a new era of precision anti-cancer medicine.
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Affiliation(s)
| | - Andrea Pession
- Pediatric Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Patrizia Hrelia
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
| | - Roberto Tonelli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy;
- Correspondence:
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24
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Gorrec F, Bellini D. The FUSION protein crystallization screen. J Appl Crystallogr 2022; 55:310-319. [PMID: 35497656 PMCID: PMC8985600 DOI: 10.1107/s1600576722001765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/15/2022] [Indexed: 11/16/2022] Open
Abstract
The success and speed of atomic structure determination of biological macromolecules by X-ray crystallography depends critically on the availability of diffraction-quality crystals. However, the process of screening crystallization conditions often consumes large amounts of sample and time. An innovative protein crystallization screen formulation called FUSION has been developed to help with the production of useful crystals. The concept behind the formulation of FUSION was to combine the most efficient components from the three MORPHEUS screens into a single screen using a systematic approach. The resulting formulation integrates 96 unique combinations of crystallization additives. Most of these additives are small molecules and ions frequently found in crystal structures of the Protein Data Bank (PDB), where they bind proteins and complexes. The efficiency of FUSION is demonstrated by obtaining high yields of diffraction-quality crystals for seven different test proteins. In the process, two crystal forms not currently in the PDB for the proteins α-amylase and avidin were discovered.
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Affiliation(s)
- Fabrice Gorrec
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
- Correspondence e-mail:
| | - Dom Bellini
- Structural Studies, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, Cambridgeshire CB2 0QH, United Kingdom
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25
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Xu Y, Yu Q, Wang P, Wu Z, Zhang L, Wu S, Li M, Wu B, Li H, Zhuang H, Zhang X, Huang Y, Gan X, Xu R. A Selective Small-Molecule c-Myc Degrader Potently Regresses Lethal c-Myc Overexpressing Tumors. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104344. [PMID: 35048559 PMCID: PMC8922104 DOI: 10.1002/advs.202104344] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/21/2021] [Indexed: 05/31/2023]
Abstract
MYC oncogene is involved in the majority of human cancers and is often associated with poor outcomes, rendering it an extraordinarily desirable target, but therapeutic targeting of c-Myc protein has been a challenge for >30 years. Here, WBC100, a novel oral active molecule glue that selectively degrades c-Myc protein over other proteins and potently kills c-Myc overexpressing cancer cells is reported. WBC100 targets the nuclear localization signal 1 (NLS1)-Basic-nuclear localization signal 2 (NLS2) region of c-Myc and induces c-Myc protein degradation through ubiquitin E3 ligase CHIP mediated 26S proteasome pathway, leading to apoptosis of cancer cells. In vivo, WBC100 potently regresses multiple lethal c-Myc overexpressing tumors such as acute myeloid leukemia, pancreatic, and gastric cancers with good tolerability in multiple xenograft mouse models. Identification of the NLS1-Basic-NLS2 region as a druggable pocket for targeting the "undruggable" c-Myc protein and that single-agent WBC100 potently regresses c-Myc overexpressing tumors through selective c-Myc proteolysis opens new perspectives for pharmacologically intervening c-Myc in human cancers.
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Affiliation(s)
- Ying Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Qingfeng Yu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Ping Wang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Zhaoxing Wu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Lei Zhang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Shuigao Wu
- Weben PharmaceuticalsHangzhou310051China
| | - Mengyuan Li
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Bowen Wu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Hongzhi Li
- Department of Molecular MedicineBeckman Research InstituteCity of Hope National Medical CenterDuarteCA91010USA
| | - Haifeng Zhuang
- Department of Hematologythe First Affiliated Hospital of Zhejiang Chinese Medical UniversityHangzhou310009China
| | - Xuzhao Zhang
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
| | - Yu Huang
- Academy of Chinese Medical SciencesZhejiang Chinese Medical UniversityHangzhou310053China
| | | | - Rongzhen Xu
- Department of Hematology and Cancer Institute (Key Laboratory of Cancer Prevention and InterventionChina National Ministry of EducationKey Laboratory of Molecular Biology in Medical SciencesThe Second Affiliated HospitalZhejiang University School of MedicineHangzhou310009China
- Institute of HematologyZhejiang UniversityHangzhou310009China
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26
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Brown IN, Lafita-Navarro MC, Conacci-Sorrell M. Regulation of Nucleolar Activity by MYC. Cells 2022; 11:cells11030574. [PMID: 35159381 PMCID: PMC8834138 DOI: 10.3390/cells11030574] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 02/02/2022] [Accepted: 02/03/2022] [Indexed: 01/20/2023] Open
Abstract
The nucleolus harbors the machinery necessary to produce new ribosomes which are critical for protein synthesis. Nucleolar size, shape, and density are highly dynamic and can be adjusted to accommodate ribosome biogenesis according to the needs for protein synthesis. In cancer, cells undergo continuous proliferation; therefore, nucleolar activity is elevated due to their high demand for protein synthesis. The transcription factor and universal oncogene MYC promotes nucleolar activity by enhancing the transcription of ribosomal DNA (rDNA) and ribosomal proteins. This review summarizes the importance of nucleolar activity in mammalian cells, MYC’s role in nucleolar regulation in cancer, and discusses how a better understanding (and the potential inhibition) of aberrant nucleolar activity in cancer cells could lead to novel therapeutics.
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Affiliation(s)
- Isabella N. Brown
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - M. Carmen Lafita-Navarro
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Correspondence: (M.C.L.-N.); (M.C.-S.)
| | - Maralice Conacci-Sorrell
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Correspondence: (M.C.L.-N.); (M.C.-S.)
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27
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Llombart V, Mansour MR. Therapeutic targeting of "undruggable" MYC. EBioMedicine 2022; 75:103756. [PMID: 34942444 PMCID: PMC8713111 DOI: 10.1016/j.ebiom.2021.103756] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/23/2021] [Accepted: 12/01/2021] [Indexed: 12/13/2022] Open
Abstract
c-MYC controls global gene expression and regulates cell proliferation, cell differentiation, cell cycle, metabolism and apoptosis. According to some estimates, MYC is dysregulated in ≈70% of human cancers and strong evidence implicates aberrantly expressed MYC in both tumor initiation and maintenance. In vivo studies show that MYC inhibition elicits a prominent anti-proliferative effect and sustained tumor regression while any alteration on healthy tissue remains reversible. This opens an exploitable window for treatment that makes MYC one of the most appealing therapeutic targets for cancer drug development. This review describes the main functional and structural features of the protein structure of MYC and provides a general overview of the most relevant or recently identified interactors that modulate MYC oncogenic activity. This review also summarizes the different approaches aiming to abrogate MYC oncogenic function, with a particular focus on the prototype inhibitors designed for the direct and indirect targeting of MYC.
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Affiliation(s)
- Victor Llombart
- UCL Cancer Institute, University College London, Department of Haematology, London WC1E 6DD, UK
| | - Marc R Mansour
- UCL Cancer Institute, University College London, Department of Haematology, London WC1E 6DD, UK; UCL Great Ormond Street Institute of Child Health, Developmental Biology and Cancer, London, UK.
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28
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Biophysical and Structural Methods to Study the bHLHZip Region of Human c-MYC. Methods Mol Biol 2021. [PMID: 34019285 DOI: 10.1007/978-1-0716-1476-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
The C-terminal region of the c-MYC transcription factor consists of approximately 100 amino acids that in its native state does not adopt a stable structure. When this region binds to the obligatory partner MAX via a coupled folding-and-binding mechanism, it forms a basic-helix-loop-helix-leucine zipper (bHLHZip) heterodimeric complex. The C-terminal region of MYC is the target for numerous drug discovery programs for direct MYC inhibition via blocking the dimerization event and/or binding to DNA, and a proper understanding of the partially folded, dynamic nature of the heterodimeric complex is essential to these efforts. The bHLHZip motif also drives protein-protein interactions with cofactors that are crucial for both transcriptional repression and activation of MYC target genes. Targeting these interactions could potentially provide a means of developing alternative approaches to halt MYC functions; however, the molecular mechanism of these regulatory interactions is poorly understood. Herein we provide methods to produce high-quality human c-MYC C-terminal by itself and in complex MAX, and how to study them using Nuclear Magnetic Resonance spectroscopy and X-ray crystallography. Our protein expression and purification protocols have already been used to study interactions with cofactors.
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29
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Radaeva M, Ton AT, Hsing M, Ban F, Cherkasov A. Drugging the 'undruggable'. Therapeutic targeting of protein-DNA interactions with the use of computer-aided drug discovery methods. Drug Discov Today 2021; 26:2660-2679. [PMID: 34332092 DOI: 10.1016/j.drudis.2021.07.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/22/2021] [Accepted: 07/17/2021] [Indexed: 02/09/2023]
Abstract
Transcription factors (TFs) act as major oncodrivers in many cancers and are frequently regarded as high-value therapeutic targets. The functionality of TFs relies on direct protein-DNA interactions, which are notoriously difficult to target with small molecules. However, this prior view of the 'undruggability' of protein-DNA interfaces has shifted substantially in recent years, in part because of significant advances in computer-aided drug discovery (CADD). In this review, we highlight recent examples of successful CADD campaigns resulting in drug candidates that directly interfere with protein-DNA interactions of several key cancer TFs, including androgen receptor (AR), ETS-related gene (ERG), MYC, thymocyte selection-associated high mobility group box protein (TOX), topoisomerase II (TOP2), and signal transducer and activator of transcription 3 (STAT3). Importantly, these findings open novel and compelling avenues for therapeutic targeting of over 1600 human TFs implicated in many conditions including and beyond cancer.
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Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Michael Hsing
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre and the Department of Urologic Sciences, University of British Columbia, 2660 Oak Street, Vancouver, BC V6H 3Z6, Canada.
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30
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Qu S, Jiao Z, Lu G, Yao B, Wang T, Rong W, Xu J, Fan T, Sun X, Yang R, Wang J, Yao Y, Xu G, Yan X, Wang T, Liang H, Zen K. PD-L1 lncRNA splice isoform promotes lung adenocarcinoma progression via enhancing c-Myc activity. Genome Biol 2021; 22:104. [PMID: 33849634 PMCID: PMC8042710 DOI: 10.1186/s13059-021-02331-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 03/25/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Although using a blockade of programmed death-ligand 1 (PD-L1) to enhance T cell immune responses shows great promise in tumor immunotherapy, the immune-checkpoint inhibition strategy is limited for patients with solid tumors. The mechanism and efficacy of such immune-checkpoint inhibition strategies in solid tumors remains unclear. RESULTS Employing qRT-PCR, Sanger sequencing, and RNA BaseScope analysis, we show that human lung adenocarcinoma (LUAD) all produce a long non-coding RNA isoform of PD-L1 (PD-L1-lnc) by alternative splicing, regardless if the tumor is positive or negative for the protein PD-L1. Similar to PD-L1 mRNA, PD-L1-lnc in various lung adenocarcinoma cells is significantly upregulated by IFNγ. Both in vitro and in vivo studies demonstrate that PD-L1-lnc increases proliferation and invasion but decreases apoptosis of lung adenocarcinoma cells. Mechanistically, PD-L1-lnc promotes lung adenocarcinoma progression through directly binding to c-Myc and enhancing c-Myc transcriptional activity. CONCLUSIONS In summary, the PD-L1 gene can generate a long non-coding RNA through alternative splicing to promote lung adenocarcinoma progression by enhancing c-Myc activity. Our results argue in favor of investigating PD-L1-lnc depletion in combination with PD-L1 blockade in lung cancer therapy.
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Affiliation(s)
- Shuang Qu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China
| | - Zichen Jiao
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Geng Lu
- Department of Emergency Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Bing Yao
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Pathology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Weiwei Rong
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Jiahan Xu
- Department of General Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Ting Fan
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Xinlei Sun
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Rong Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China
| | - Jun Wang
- Department of Emergency Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Yongzhong Yao
- Department of General Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Guifang Xu
- Department of Gastroenterology, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Xin Yan
- Department of Respiratory Medicine, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China
| | - Tao Wang
- Department of Thoracic Surgery, Nanjing Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Hongwei Liang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China.
- School of Life Science and Technology, China Pharmaceutical University, Nanjing, China.
| | - Ke Zen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing, China.
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31
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Pellanda P, Dalsass M, Filipuzzi M, Loffreda A, Verrecchia A, Castillo Cano V, Thabussot H, Doni M, Morelli MJ, Soucek L, Kress T, Mazza D, Mapelli M, Beaulieu ME, Amati B, Sabò A. Integrated requirement of non-specific and sequence-specific DNA binding in Myc-driven transcription. EMBO J 2021; 40:e105464. [PMID: 33792944 DOI: 10.15252/embj.2020105464] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 02/15/2021] [Accepted: 02/24/2021] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic transcription factors recognize specific DNA sequence motifs, but are also endowed with generic, non-specific DNA-binding activity. How these binding modes are integrated to determine select transcriptional outputs remains unresolved. We addressed this question by site-directed mutagenesis of the Myc transcription factor. Impairment of non-specific DNA backbone contacts caused pervasive loss of genome interactions and gene regulation, associated with increased intra-nuclear mobility of the Myc protein in murine cells. In contrast, a mutant lacking base-specific contacts retained DNA-binding and mobility profiles comparable to those of the wild-type protein, but failed to recognize its consensus binding motif (E-box) and could not activate Myc-target genes. Incidentally, this mutant gained weak affinity for an alternative motif, driving aberrant activation of different genes. Altogether, our data show that non-specific DNA binding is required to engage onto genomic regulatory regions; sequence recognition in turn contributes to transcriptional activation, acting at distinct levels: stabilization and positioning of Myc onto DNA, and-unexpectedly-promotion of its transcriptional activity. Hence, seemingly pervasive genome interaction profiles, as detected by ChIP-seq, actually encompass diverse DNA-binding modalities, driving defined, sequence-dependent transcriptional responses.
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Affiliation(s)
- Paola Pellanda
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy.,Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Mattia Dalsass
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Alessia Loffreda
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | | | - Virginia Castillo Cano
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain
| | | | - Mirko Doni
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Marco J Morelli
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Laura Soucek
- Peptomyc S.L., Barcelona, Spain.,Vall d'Hebron Institute of Oncology (VHIO), Edifici Cellex, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.,Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Theresia Kress
- Center for Genomic Science of IIT@SEMM, Fondazione Istituto Italiano di Tecnologia (IIT), Milan, Italy
| | - Davide Mazza
- Experimental Imaging Center, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marina Mapelli
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | | | - Bruno Amati
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
| | - Arianna Sabò
- European Institute of Oncology (IEO) - IRCCS, Milan, Italy
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32
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Kiss L, Clift D, Renner N, Neuhaus D, James LC. RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination. Nat Commun 2021; 12:1220. [PMID: 33619271 PMCID: PMC7900206 DOI: 10.1038/s41467-021-21443-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/26/2021] [Indexed: 12/24/2022] Open
Abstract
Attachment of ubiquitin (Ub) to proteins is one of the most abundant and versatile of all posttranslational modifications and affects outcomes in essentially all physiological processes. RING E3 ligases target E2 Ub-conjugating enzymes to the substrate, resulting in its ubiquitination. However, the mechanism by which a ubiquitin chain is formed on the substrate remains elusive. Here we demonstrate how substrate binding can induce a specific RING topology that enables self-ubiquitination. By analyzing a catalytically trapped structure showing the initiation of TRIM21 RING-anchored ubiquitin chain elongation, and in combination with a kinetic study, we illuminate the chemical mechanism of ubiquitin conjugation. Moreover, biochemical and cellular experiments show that the topology found in the structure can be induced by substrate binding. Our results provide insights into ubiquitin chain formation on a structural, biochemical and cellular level with broad implications for targeted protein degradation.
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Affiliation(s)
- Leo Kiss
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Dean Clift
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Leo C James
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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33
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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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34
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The Molecular 'Myc-anisms' Behind Myc-Driven Tumorigenesis and the Relevant Myc-Directed Therapeutics. Int J Mol Sci 2020; 21:ijms21249486. [PMID: 33322239 PMCID: PMC7764474 DOI: 10.3390/ijms21249486] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/09/2020] [Accepted: 12/11/2020] [Indexed: 02/07/2023] Open
Abstract
MYC, a well-studied proto-oncogene that is overexpressed in >20% of tumors across all cancers, is classically known as “undruggable” due to its crucial roles in cell processes and its lack of a drug binding pocket. Four decades of research and creativity led to the discovery of a myriad of indirect (and now some direct!) therapeutic strategies targeting Myc. This review explores the various mechanisms in which Myc promotes cancer and highlights five key therapeutic approaches to disrupt Myc, including transcription, Myc-Max dimerization, protein stability, cell cycle regulation, and metabolism, in order to develop more specific Myc-directed therapies.
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Sicoli G, Kress T, Vezin H, Ledolter K, Kurzbach D. A Switch between Two Intrinsically Disordered Conformational Ensembles Modulates the Active Site of a Basic-Helix-Loop-Helix Transcription Factor. J Phys Chem Lett 2020; 11:8944-8951. [PMID: 33030907 PMCID: PMC7649839 DOI: 10.1021/acs.jpclett.0c02242] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
We report a conformational switch between two distinct intrinsically disordered subensembles within the active site of a transcription factor. This switch highlights an evolutionary benefit conferred by the high plasticity of intrinsically disordered domains, namely, their potential to dynamically sample a heterogeneous conformational space housing multiple states with tailored properties. We focus on proto-oncogenic basic-helix-loop-helix (bHLH)-type transcription factors, as these play key roles in cell regulation and function. Despite intense research efforts, the understanding of structure-function relations of these transcription factors remains incomplete as they feature intrinsically disordered DNA-interaction domains that are difficult to characterize, theoretically as well as experimentally. Here we characterize the structural dynamics of the intrinsically disordered region DNA-binding site of the vital MYC-associated transcription factor X (MAX). Integrating nuclear magnetic resonance (NMR) measurements, molecular dynamics (MD) simulations, and electron paramagnetic resonance (EPR) measurements, we show that, in the absence of DNA, the binding site of the free MAX2 homodimer samples two intrinsically disordered conformational subensembles. These feature distinct structural properties: one subensemble consists of a set of highly flexible and spatially extended conformers, while the second features a set of "hinged" conformations. In this latter ensemble, the disordered N-terminal tails of MAX2 fold back along the dimer, forming transient long-range contacts with the HLH-region and thereby exposing the DNA binding site to the solvent. The features of these divergent substates suggest two mechanisms by which protein conformational dynamics in MAX2 might modulate DNA-complex formation: by enhanced initial recruitment of free DNA ligands, as a result of the wider conformational space sampled by the extended ensemble, and by direct exposure of the binding site and the corresponding strong electrostatic attractions presented while in the hinged conformations.
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Affiliation(s)
- Giuseppe Sicoli
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Thomas Kress
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.
| | - Hervé Vezin
- Laboratoire
Avancé de Spectroscopie pour les Interactions, la Réactivité
et l’Environnement (LASIRE), UMR CNRS 8516, Université de Lille, Avenue Paul Langevin − C4, F-59655 Villeneuve d’Ascq, France
| | - Karin Ledolter
- Department
for Structural and Computational Biology, Max F. Perutz Laboratories, University Vienna, Campus Vienna BioCenter 5, 1030 Vienna, Austria
| | - Dennis Kurzbach
- Faculty
of Chemistry, Institute of Biological Chemistry, University of Vienna, Währinger Str. 38, 1090 Vienna, Austria
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Beaulieu ME, Castillo F, Soucek L. Structural and Biophysical Insights into the Function of the Intrinsically Disordered Myc Oncoprotein. Cells 2020; 9:E1038. [PMID: 32331235 PMCID: PMC7226237 DOI: 10.3390/cells9041038] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/16/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
Myc is a transcription factor driving growth and proliferation of cells and involved in the majority of human tumors. Despite a huge body of literature on this critical oncogene, our understanding of the exact molecular determinants and mechanisms that underlie its function is still surprisingly limited. Indubitably though, its crucial and non-redundant role in cancer biology makes it an attractive target. However, achieving successful clinical Myc inhibition has proven challenging so far, as this nuclear protein is an intrinsically disordered polypeptide devoid of any classical ligand binding pockets. Indeed, Myc only adopts a (partially) folded structure in some contexts and upon interacting with some protein partners, for instance when dimerizing with MAX to bind DNA. Here, we review the cumulative knowledge on Myc structure and biophysics and discuss the implications for its biological function and the development of improved Myc inhibitors. We focus this biophysical walkthrough mainly on the basic region helix-loop-helix leucine zipper motif (bHLHLZ), as it has been the principal target for inhibitory approaches so far.
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Affiliation(s)
| | | | - Laura Soucek
- Peptomyc S.L., Edifici Cellex, 08035 Barcelona, Spain; (F.C.); (L.S.)
- Vall d’Hebron Institute of Oncology (VHIO), Edifici Cellex, 08035 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08035 Barcelona, Spain
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08035 Bellaterra, Spain
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