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Zhang Q, Fan S, Tang M, Wang C, Li X, Jin Y, Yang Z. Computation-Guided Rational Design of Cysteine-Less Protein Variants in Engineered hCGL. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9937-9946. [PMID: 38651303 DOI: 10.1021/acs.jafc.3c06821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The engineered human cystathionine-γ-lyase (hCGL) resulting in enhanced activity toward both cysteine and cystine unveils a potential robust antitumor activity. However, the presence of cysteine residues has the potential to induce oligomerization or incorrect disulfide bonding, which may decrease the bioavailability of biopharmaceuticals. Through a meticulous design process targeting the cysteine residues within engineered hCGL, a set of potential beneficial mutants were obtained by virtual screening employing Rosetta and ABACUS. Experimental measurements have revealed that most of the mutants showed increased activity toward both substrates l-Cys and CSSC. Furthermore, mutants C109V and C229D demonstrated Tm value increases of 8.2 and 1.8 °C, respectively. After an 80 min incubation at 60 °C, mutant C229D still maintained high residual activity. Unexpectedly, mutant C109V, displaying activity approximately 2-fold higher than the activity of wild type (WT) for both substrates, showed disappointing instability in plasma, which suggests that computational design still requires further consideration. Analysis of their structure and molecular dynamics (MD) simulation revealed the impact of hydrophobic interaction, hydrogen bonds, and near-attack conformation (NAC) stability on activity and stability. This study acquired information about mutants that exhibit enhanced activity or thermal resistance and serve as valuable guidance for subsequent specific cysteine modifications.
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Affiliation(s)
- Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mengjia Tang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Chenyu Wang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaoxiao Li
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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2
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Fu J, Zhang J, Chen X, Liu Z, Yang X, He Z, Hao Y, Liu B, Yao D. ATPase family AAA domain-containing protein 2 (ATAD2): From an epigenetic modulator to cancer therapeutic target. Theranostics 2023; 13:787-809. [PMID: 36632213 PMCID: PMC9830439 DOI: 10.7150/thno.78840] [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: 09/12/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
ATPase family AAA domain-containing protein 2 (ATAD2) has been widely reported to be a new emerging oncogene that is closely associated with epigenetic modifications in human cancers. As a coactivator of transcription factors, ATAD2 can participate in epigenetic modifications and regulate the expression of downstream oncogenes or tumor suppressors, which may be supported by the enhancer of zeste homologue 2. Moreover, the dominant structure (AAA + ATPase and bromine domains) can make ATAD2 a potential therapeutic target in cancer, and some relevant small-molecule inhibitors, such as GSK8814 and AZ13824374, have also been discovered. Thus, in this review, we focus on summarizing the structural features and biological functions of ATAD2 from an epigenetic modulator to a cancer therapeutic target, and further discuss the existing small-molecule inhibitors targeting ATAD2 to improve potential cancer therapy. Together, these inspiring findings would shed new light on ATAD2 as a promising druggable target in cancer and provide a clue on the development of candidate anticancer drugs.
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Affiliation(s)
- Jiahui Fu
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.,State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jin Zhang
- School of Pharmaceutical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xiya Chen
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.,School of Pharmaceutical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Zhiying Liu
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.,School of Pharmaceutical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China
| | - Xuetao Yang
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Zhendan He
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China
| | - Yue Hao
- School of Pharmaceutical Sciences, Medical School, Shenzhen University, Shenzhen 518060, China.,✉ Corresponding authors: E-mail addresses: (Yue Hao); (Bo Liu), or (Dahong Yao). Tel./Fax. (+86)-28-85164063
| | - Bo Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, China.,✉ Corresponding authors: E-mail addresses: (Yue Hao); (Bo Liu), or (Dahong Yao). Tel./Fax. (+86)-28-85164063
| | - Dahong Yao
- School of Pharmaceutical Sciences, Shenzhen Technology University, Shenzhen, 518118, China.,✉ Corresponding authors: E-mail addresses: (Yue Hao); (Bo Liu), or (Dahong Yao). Tel./Fax. (+86)-28-85164063
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3
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Davison G, Martin MP, Turberville S, Dormen S, Heath R, Heptinstall AB, Lawson M, Miller DC, Ng YM, Sanderson JN, Hope I, Wood DJ, Cano C, Endicott JA, Hardcastle IR, Noble MEM, Waring MJ. Mapping Ligand Interactions of Bromodomains BRD4 and ATAD2 with FragLites and PepLites─Halogenated Probes of Druglike and Peptide-like Molecular Interactions. J Med Chem 2022; 65:15416-15432. [PMID: 36367089 PMCID: PMC9706561 DOI: 10.1021/acs.jmedchem.2c01357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 11/13/2022]
Abstract
The development of ligands for biological targets is critically dependent on the identification of sites on proteins that bind molecules with high affinity. A set of compounds, called FragLites, can identify such sites, along with the interactions required to gain affinity, by X-ray crystallography. We demonstrate the utility of FragLites in mapping the binding sites of bromodomain proteins BRD4 and ATAD2 and demonstrate that FragLite mapping is comparable to a full fragment screen in identifying ligand binding sites and key interactions. We extend the FragLite set with analogous compounds derived from amino acids (termed PepLites) that mimic the interactions of peptides. The output of the FragLite maps is shown to enable the development of ligands with leadlike potency. This work establishes the use of FragLite and PepLite screening at an early stage in ligand discovery allowing the rapid assessment of tractability of protein targets and informing downstream hit-finding.
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Affiliation(s)
- Gemma Davison
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Mathew P. Martin
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Shannon Turberville
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Selma Dormen
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Richard Heath
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Amy B. Heptinstall
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Marie Lawson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Duncan C. Miller
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Yi Min Ng
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - James N. Sanderson
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Ian Hope
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Daniel J. Wood
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Céline Cano
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Jane A. Endicott
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Ian R. Hardcastle
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
| | - Martin E. M. Noble
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O’Gorman Building, Framlington Place, Newcastle upon Tyne NE2 4AD, U.K.
| | - Michael J. Waring
- Cancer
Research Horizons Therapeutic Innovation, Newcastle Drug Discovery
Unit, Newcastle University Centre for Cancer, Chemistry, School of
Natural and Environmental Sciences, Newcastle
University, Bedson Building, Newcastle upon Tyne NE1 7RU, U.K.
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4
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Fritz AJ, El Dika M, Toor RH, Rodriguez PD, Foley SJ, Ullah R, Nie D, Banerjee B, Lohese D, Glass KC, Frietze S, Ghule PN, Heath JL, Imbalzano AN, van Wijnen A, Gordon J, Lian JB, Stein JL, Stein GS, Stein GS. Epigenetic-Mediated Regulation of Gene Expression for Biological Control and Cancer: Cell and Tissue Structure, Function, and Phenotype. Results Probl Cell Differ 2022; 70:339-373. [PMID: 36348114 PMCID: PMC9753575 DOI: 10.1007/978-3-031-06573-6_12] [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: 11/09/2022]
Abstract
Epigenetic gene regulatory mechanisms play a central role in the biological control of cell and tissue structure, function, and phenotype. Identification of epigenetic dysregulation in cancer provides mechanistic into tumor initiation and progression and may prove valuable for a variety of clinical applications. We present an overview of epigenetically driven mechanisms that are obligatory for physiological regulation and parameters of epigenetic control that are modified in tumor cells. The interrelationship between nuclear structure and function is not mutually exclusive but synergistic. We explore concepts influencing the maintenance of chromatin structures, including phase separation, recognition signals, factors that mediate enhancer-promoter looping, and insulation and how these are altered during the cell cycle and in cancer. Understanding how these processes are altered in cancer provides a potential for advancing capabilities for the diagnosis and identification of novel therapeutic targets.
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Affiliation(s)
- Andrew J. Fritz
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Mohammed El Dika
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rabail H. Toor
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | | | - Stephen J. Foley
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Rahim Ullah
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Daijing Nie
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Bodhisattwa Banerjee
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Dorcas Lohese
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Karen C. Glass
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Pharmacology, Burlington, VT 05405
| | - Seth Frietze
- University of Vermont, College of Nursing and Health Sciences, Burlington, VT 05405
| | - Prachi N. Ghule
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jessica L. Heath
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405,University of Vermont, Larner College of Medicine, Department of Pediatrics, Burlington, VT 05405
| | - Anthony N. Imbalzano
- UMass Chan Medical School, Department of Biochemistry and Molecular Biotechnology, Worcester, MA 01605
| | - Andre van Wijnen
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jonathan Gordon
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Jane B. Lian
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Janet L. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
| | - Gary S. Stein
- University of Vermont, UVM Cancer Center, Larner College of Medicine, Department of Biochemistry, Burlington, VT 05405
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5
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Boyson SP, Gao C, Quinn K, Boyd J, Paculova H, Frietze S, Glass KC. Functional Roles of Bromodomain Proteins in Cancer. Cancers (Basel) 2021; 13:3606. [PMID: 34298819 PMCID: PMC8303718 DOI: 10.3390/cancers13143606] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/09/2021] [Accepted: 07/09/2021] [Indexed: 12/31/2022] Open
Abstract
Histone acetylation is generally associated with an open chromatin configuration that facilitates many cellular processes including gene transcription, DNA repair, and DNA replication. Aberrant levels of histone lysine acetylation are associated with the development of cancer. Bromodomains represent a family of structurally well-characterized effector domains that recognize acetylated lysines in chromatin. As part of their fundamental reader activity, bromodomain-containing proteins play versatile roles in epigenetic regulation, and additional functional modules are often present in the same protein, or through the assembly of larger enzymatic complexes. Dysregulated gene expression, chromosomal translocations, and/or mutations in bromodomain-containing proteins have been correlated with poor patient outcomes in cancer. Thus, bromodomains have emerged as a highly tractable class of epigenetic targets due to their well-defined structural domains, and the increasing ease of designing or screening for molecules that modulate the reading process. Recent developments in pharmacological agents that target specific bromodomains has helped to understand the diverse mechanisms that bromodomains play with their interaction partners in a variety of chromatin processes, and provide the promise of applying bromodomain inhibitors into the clinical field of cancer treatment. In this review, we explore the expression and protein interactome profiles of bromodomain-containing proteins and discuss them in terms of functional groups. Furthermore, we highlight our current understanding of the roles of bromodomain-containing proteins in cancer, as well as emerging strategies to specifically target bromodomains, including combination therapies using bromodomain inhibitors alongside traditional therapeutic approaches designed to re-program tumorigenesis and metastasis.
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Affiliation(s)
- Samuel P. Boyson
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
| | - Cong Gao
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Kathleen Quinn
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Joseph Boyd
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (C.G.); (J.B.); (H.P.)
- University of Vermont Cancer Center, Burlington, VT 05405, USA
| | - Karen C. Glass
- Department of Pharmaceutical Sciences, Albany College of Pharmacy and Health Sciences, Colchester, VT 05446, USA;
- Department of Pharmacology, Larner College of Medicine, University of Vermont, Burlington, VT 05405, USA;
- University of Vermont Cancer Center, Burlington, VT 05405, USA
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6
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Zhang G, Li S, Cheng KW, Chou TF. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Eur J Med Chem 2021; 219:113446. [PMID: 33873056 PMCID: PMC8165034 DOI: 10.1016/j.ejmech.2021.113446] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/21/2021] [Accepted: 03/30/2021] [Indexed: 01/07/2023]
Abstract
ATPases Associated with Diverse Cellular Activity (AAA ATPase) are essential enzymes found in all organisms. They are involved in various processes such as DNA replication, protein degradation, membrane fusion, microtubule serving, peroxisome biogenesis, signal transduction, and the regulation of gene expression. Due to the importance of AAA ATPases, several researchers identified and developed small-molecule inhibitors against these enzymes. We discuss six AAA ATPases that are potential drug targets and have well-developed inhibitors. We compare available structures that suggest significant differences of the ATP binding pockets among the AAA ATPases with or without ligand. The distances from ADP to the His20 in the His-Ser-His motif and the Arg finger (Arg353 or Arg378) in both RUVBL1/2 complex structures bound with or without ADP have significant differences, suggesting dramatically different interactions of the binding site with ADP. Taken together, the inhibitors of six well-studied AAA ATPases and their structural information suggest further development of specific AAA ATPase inhibitors due to difference in their structures. Future chemical biology coupled with proteomic approaches could be employed to develop variant specific, complex specific, and pathway specific inhibitors or activators for AAA ATPase proteins.
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Affiliation(s)
- Gang Zhang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
| | - Shan Li
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Kai-Wen Cheng
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States
| | - Tsui-Fen Chou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, 91125, United States.
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7
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Dolbois A, Batiste L, Wiedmer L, Dong J, Brütsch M, Huang D, Deerain NM, Spiliotopoulos D, Cheng-Sánchez I, Laul E, Nevado C, Śledź P, Caflisch A. Hitting a Moving Target: Simulation and Crystallography Study of ATAD2 Bromodomain Blockers. ACS Med Chem Lett 2020; 11:1573-1580. [PMID: 32832026 DOI: 10.1021/acsmedchemlett.0c00080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022] Open
Abstract
Small molecule ligand binding to the ATAD2 bromodomain is investigated here through the synergistic combination of molecular dynamics and protein crystallography. A previously unexplored conformation of the binding pocket upon rearrangement of the gatekeeper residue Ile1074 has been found. Further, our investigations reveal how minor structural differences in the ligands result in binding with different plasticity of the ZA loop for this difficult-to-drug bromodomain.
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Affiliation(s)
- Aymeric Dolbois
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Laurent Batiste
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lars Wiedmer
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jing Dong
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Manuela Brütsch
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Danzhi Huang
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Nicholas M Deerain
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Iván Cheng-Sánchez
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Eleen Laul
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Cristina Nevado
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Paweł Śledź
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Amedeo Caflisch
- Department of Chemistry and Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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8
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Abstract
Bromodomain-containing proteins are often part of chromatin-modifying complexes, and their activity can lead to altered expression of genes that drive cancer, inflammation and neurological disorders in humans. Bromodomain-PHD finger protein 1 (BRPF1) is part of the MOZ (monocytic leukemic zinc-finger protein) HAT (histone acetyltransferase) complex, which is associated with chromosomal translocations known to contribute to the development of acute myeloid leukemia (AML). BRPF1 contains a unique combination of chromatin reader domains including two plant homeodomain (PHD) fingers separated by a zinc knuckle (PZP domain), a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. BRPF1 is known to recruit the MOZ HAT complex to chromatin by recognizing acetylated lysine residues on the N-terminal histone tail region through its bromodomain. However, histone proteins can contain several acetylation modifications on their N-terminus, and it is unknown how additional marks influence bromodomain recruitment to chromatin. Here, we identify the BRPF1 bromodomain as a selective reader of di-acetyllysine modifications on histone H4. We used ITC assays to characterize the binding of di-acetylated histone ligands to the BRPF1 bromodomain and found that the domain binds preferentially to histone peptides H4K5acK8ac and H4K5acK12ac. Analytical ultracentrifugation (AUC) experiments revealed that the monomeric state of the BRPF1 bromodomain coordinates di-acetylated histone ligands. NMR chemical shift perturbation studies, along with binding and mutational analyses, revealed non-canonical regions of the bromodomain-binding pocket that are important for histone tail recognition. Together, our findings provide critical information on how the combinatorial action of post-translational modifications can modulate BRPF1 bromodomain binding and specificity.
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9
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Bamborough P, Chung CW, Demont EH, Bridges AM, Craggs PD, Dixon DP, Francis P, Furze RC, Grandi P, Jones EJ, Karamshi B, Locke K, Lucas SCC, Michon AM, Mitchell DJ, Pogány P, Prinjha RK, Rau C, Roa AM, Roberts AD, Sheppard RJ, Watson RJ. A Qualified Success: Discovery of a New Series of ATAD2 Bromodomain Inhibitors with a Novel Binding Mode Using High-Throughput Screening and Hit Qualification. J Med Chem 2019; 62:7506-7525. [PMID: 31398032 DOI: 10.1021/acs.jmedchem.9b00673] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bromodomain of ATAD2 has proved to be one of the least-tractable proteins within this target class. Here, we describe the discovery of a new class of inhibitors by high-throughput screening and show how the difficulties encountered in establishing a screening triage capable of finding progressible hits were overcome by data-driven optimization. Despite the prevalence of nonspecific hits and an exceptionally low progressible hit rate (0.001%), our optimized hit qualification strategy employing orthogonal biophysical methods enabled us to identify a single active series. The compounds have a novel ATAD2 binding mode with noncanonical features including the displacement of all conserved water molecules within the active site and a halogen-bonding interaction. In addition to reporting this new series and preliminary structure-activity relationship, we demonstrate the value of diversity screening to complement the knowledge-based approach used in our previous ATAD2 work. We also exemplify tactics that can increase the chance of success when seeking new chemical starting points for novel and less-tractable targets.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Paola Grandi
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | | | | | | | | | | | | | | | | | - Christina Rau
- Cellzome , Meyerhofstrasse 1 , Heidelberg 69117 , Germany
| | - Ana Maria Roa
- GlaxoSmithKline Tres Cantos , 28760 Tres Cantos , Madrid , Spain
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