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Malone HA, Roberts CWM. Chromatin remodellers as therapeutic targets. Nat Rev Drug Discov 2024; 23:661-681. [PMID: 39014081 DOI: 10.1038/s41573-024-00978-5] [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] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Large-scale cancer genome sequencing studies have revealed that chromatin regulators are frequently mutated in cancer. In particular, more than 20% of cancers harbour mutations in genes that encode subunits of SWI/SNF (BAF) chromatin remodelling complexes. Additional links of SWI/SNF complexes to disease have emerged with the findings that some oncogenes drive transformation by co-opting SWI/SNF function and that germline mutations in select SWI/SNF subunits are the basis of several neurodevelopmental disorders. Other chromatin remodellers, including members of the ISWI, CHD and INO80/SWR complexes, have also been linked to cancer and developmental disorders. Consequently, therapeutic manipulation of SWI/SNF and other remodelling complexes has become of great interest, and drugs that target SWI/SNF subunits have entered clinical trials. Genome-wide perturbation screens in cancer cell lines with SWI/SNF mutations have identified additional synthetic lethal targets and led to further compounds in clinical trials, including one that has progressed to FDA approval. Here, we review the progress in understanding the structure and function of SWI/SNF and other chromatin remodelling complexes, mechanisms by which SWI/SNF mutations cause cancer and neurological diseases, vulnerabilities that arise because of these mutations and efforts to target SWI/SNF complexes and synthetic lethal targets for therapeutic benefit.
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Affiliation(s)
- Hayden A Malone
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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2
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Li F, Yu J, Pan T, Feng H, Li J, Yu B, Fan Z, Sang Q, Chen M, Zang M, Hou J, Wu X, Yu Y, Li Y, Yan C, Zhu Z, Su L, Liu B. BPTF Drives Gastric Cancer Resistance to EGFR Inhibitor by Epigenetically Regulating the C-MYC/PLCG1/Perk Axis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2303091. [PMID: 37863665 PMCID: PMC10700682 DOI: 10.1002/advs.202303091] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Revised: 08/06/2023] [Indexed: 10/22/2023]
Abstract
Erlotinib, an EGFR tyrosine kinase inhibitor, is used for treating patients with cancer exhibiting EGFR overexpression or mutation. However, the response rate of erlotinib is low among patients with gastric cancer (GC). The findings of this study illustrated that the overexpression of bromodomain PHD finger transcription factor (BPTF) is partially responsible for erlotinib resistance in GC, and the combination of the BPTF inhibitor AU-1 with erlotinib synergistically inhibited tumor growth both in vivo and in vitro. AU-1 inhibited the epigenetic function of BPTF and decreased the transcriptional activity of c-MYC on PLCG1 by attenuating chromosome accessibility of the PLCG1 promoter region, thus decreasing the expression of p-PLCG1 and p-Erk and eventually improving the sensitivity of GC cells to erlotinib. In patient-derived xenograft (PDX) models, AU-1 monotherapy exhibited remarkable tumor-inhibiting activity and is synergistic anti-tumor effects when combined with erlotinib. Altogether, the findings illustrate that BPTF affects the responsiveness of GC to erlotinib by epigenetically regulating the c-MYC/PLCG1/pErk axis, and the combination of BPTF inhibitors and erlotinib is a viable therapeutic approach for GC.
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Affiliation(s)
- Fangyuan Li
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Junxian Yu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Tao Pan
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Haoran Feng
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Jianfang Li
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Beiqin Yu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Zhiyuan Fan
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Qingqing Sang
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Mengdi Chen
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Mingde Zang
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
- Department of Gastric Cancer SurgeryFudan University Shanghai Cancer CenterDepartment of OncologyShanghai Medical CollegeFudan UniversityShanghai200032P. R. China
| | - Junyi Hou
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Xiongyan Wu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Yingyan Yu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Yuan‐Yuan Li
- Shanghai Center for Bioinformation TechnologyShanghai Engineering Research Center of Pharmaceutical Translation & Shanghai Industrial Technology InstituteShanghai202163P. R. China
| | - Chao Yan
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Zhenggang Zhu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Liping Su
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
| | - Bingya Liu
- Department of General SurgeryShanghai Key Laboratory of Gastric NeoplasmsShanghai Institute of Digestive SurgeryRuijin HospitalShanghai Jiao Tong University School of MedicineShanghai200025P. R. China
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3
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Jiang C, Yang Y, He S, Yue Z, Xing T, Chu P, Yang W, Chen H, Zhao X, Yu Y, Zhang X, Su Y, Guo Y, Ma X. BPTF in bone marrow provides a potential progression biomarker regulated by TFAP4 through the PI3K/AKT pathway in neuroblastoma. Biol Proced Online 2023; 25:11. [PMID: 37170211 PMCID: PMC10176855 DOI: 10.1186/s12575-023-00200-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 04/18/2023] [Indexed: 05/13/2023] Open
Abstract
BACKGROUND Neuroblastoma (NB) is the most common extracranial malignant solid tumor in children, which is highly prone to bone marrow (BM) metastasis. BM can monitor early signs of mild disease and metastasis. Existing biomarkers are insufficient for the diagnosis and treatment of NB. Bromodomain PHD finger transcription factor (BPTF) is an important subunit of the chromatin-remodeling complex that is closely associated with tumors. Here, we evaluated whether BPTF in BM plays an important role in predicting NB progression, and explore the molecular mechanism of BPTF in NB. METHODS The clinical relevance of the BPTF was predicted in the GEO (GSE62564) and TARGET database. The biological function of BPTF in NB was investigated by constructing cell lines and employing BPTF inhibitor AU1. Western blot was used to determine the changes of BPTF, TFAP4, PI3K/AKT signaling and Epithelial-mesenchymal transition (EMT) related markers. A total of 109 children with newly diagnosed NB in Beijing Children's Hospital from January 2018 to March 2021 were included in this study. RT-PCR was used to measure the BPTF and TFAP4 expression in BM. The cut-off level was set at the median value of BPTF expression levels. RESULTS Databases suggested that BPTF expression was higher in NB and was significantly associated with stage and grade. Proliferation and migration of NB cells were slowed down when BPTF was silenced. Mechanistically, TFAP4 could positively regulate BPTF and promotes EMT process through activating the PI3K/AKT signaling pathway. Moreover, detection of the newly diagnosed BM specimens showed that BPTF expression was significantly higher in high-risk group, stage IV group and BM metastasis group. Children with high BPTF at initial diagnosis were considered to have high risk for disease progression and recurrence. BPTF is an independent risk factor for predicting NB progression. CONCLUSIONS A novel and convenient BPTF-targeted humoral detection that can prompt minimal residual and predict NB progression in the early stages of the disease were identified. BPTF inhibitor AU1 is expected to become a new targeted drug for NB therapy. It's also reveal previously unknown mechanisms of BPTF in NB cell proliferation and metastasis through TFAP4 and PI3K/AKT pathways.
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Affiliation(s)
- Chiyi Jiang
- Medical Oncology Department, Pediatric Oncology CenterNational Center for Children's HealthKey Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, Xicheng District, China
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Yeran Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Sidou He
- Medical Oncology Department, Pediatric Oncology CenterNational Center for Children's HealthKey Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Zhixia Yue
- Hematologic Disease LaboratoryKey Laboratory of Pediatric Hematology OncologyNational Key Discipline of Pediatrics (Capital Medical University)Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Hematology Center, Beijing, China
| | - Tianyu Xing
- Hematologic Disease LaboratoryKey Laboratory of Pediatric Hematology OncologyNational Key Discipline of Pediatrics (Capital Medical University)Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Hematology Center, Beijing, China
| | - Ping Chu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Wenfa Yang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Hui Chen
- Hematologic Disease LaboratoryKey Laboratory of Pediatric Hematology OncologyNational Key Discipline of Pediatrics (Capital Medical University)Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Hematology Center, Beijing, China
| | - Xiaoxi Zhao
- Hematologic Disease LaboratoryKey Laboratory of Pediatric Hematology OncologyNational Key Discipline of Pediatrics (Capital Medical University)Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Hematology Center, Beijing, China
| | - Yongbo Yu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Xuan Zhang
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China
| | - Yan Su
- Medical Oncology Department, Pediatric Oncology CenterNational Center for Children's HealthKey Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, Xicheng District, China.
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, MOE Key Laboratory of Major Diseases in Children, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, 56 Nanlishi Road, Beijing, Xicheng District, China.
| | - Xiaoli Ma
- Medical Oncology Department, Pediatric Oncology CenterNational Center for Children's HealthKey Laboratory of Pediatric Hematology Oncology, Key Laboratory of Major Diseases in Children, Ministry of Education, Beijing Children's Hospital, Capital Medical University, 56 Nanlishi Road, Beijing, Xicheng District, China.
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4
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Dixon T, Lotz SD, Dickson A. Creating Maps of the Ligand Binding Landscape for Kinetics-Based Drug Discovery. Methods Mol Biol 2022; 2385:325-334. [PMID: 34888727 DOI: 10.1007/978-1-0716-1767-0_15] [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] [Indexed: 06/13/2023]
Abstract
Simulations of ligand-protein interactions can be very useful for drug design and to gain biological insight. Full pathways of ligand-protein binding can be used to get information about ligand binding transition states, which form the rate-limiting step of the binding and release processes. However, these simulations are typically limited by the presence of large energy barriers that separate stable poses of interest. Here we describe a simulation protocol for exploring and analyzing landscapes of ligand-protein interactions that makes use of molecular docking, enhanced molecular simulation with the weighted ensemble algorithm, and network analysis. It can be accomplished using a modest cluster of graphics processing units and freely accessible software. This protocol focuses on the construction and analysis of a network model of ligand binding poses and provides links to resources that describe the other steps in more detail. The end result of this protocol is a map of the ligand-protein binding landscape that identifies transition states of the ligand binding pathway, as well as alternative bound poses that could be stabilized with modifications to the ligand.
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Affiliation(s)
- Tom Dixon
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA
| | - Samuel D Lotz
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA
- Roivant Sciences, New York, NY, USA
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, USA.
- Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, USA.
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5
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Buchholz CR, Pomerantz WCK. 19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery. RSC Chem Biol 2021; 2:1312-1330. [PMID: 34704040 PMCID: PMC8496043 DOI: 10.1039/d1cb00085c] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Accepted: 07/07/2021] [Indexed: 12/28/2022] Open
Abstract
19F NMR has emerged as a powerful tool in drug discovery, particularly in fragment-based screens. The favorable magnetic resonance properties of the fluorine-19 nucleus, the general absence of fluorine in biological settings, and its ready incorporation into both small molecules and biopolymers, has enabled multiple applications of 19F NMR using labeled small molecules and proteins in biophysical, biochemical, and cellular experiments. This review will cover developments in ligand-observed and protein-observed 19F NMR experiments tailored towards drug discovery with a focus on fragment screening. We also cover the key advances that have furthered the field in recent years, including quantitative, structural, and in-cell methodologies. Several case studies are described for each application to highlight areas for innovation and to further catalyze new NMR developments for using this versatile nucleus.
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Affiliation(s)
- Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
| | - William C K Pomerantz
- Department of Medicinal Chemistry, University of Minnesota 308 Harvard Street SE Minneapolis Minnesota 55455 USA
- Department of Chemistry, University of Minnesota 207 Pleasant St. SE Minneapolis Minnesota 55455 USA
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6
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Zahid H, Buchholz CR, Singh M, Ciccone MF, Chan A, Nithianantham S, Shi K, Aihara H, Fischer M, Schönbrunn E, Dos Santos CO, Landry JW, Pomerantz WCK. New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. J Med Chem 2021; 64:13902-13917. [PMID: 34515477 DOI: 10.1021/acs.jmedchem.1c01294] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (Kd = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.
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Affiliation(s)
- Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Manjulata Singh
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Michael F Ciccone
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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7
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Lu T, Lu H, Duan Z, Wang J, Han J, Xiao S, Chen H, Jiang H, Chen Y, Yang F, Li Q, Chen D, Lin J, Li B, Jiang H, Chen K, Lu W, Lin H, Luo C. Discovery of High-Affinity Inhibitors of the BPTF Bromodomain. J Med Chem 2021; 64:12075-12088. [PMID: 34375106 DOI: 10.1021/acs.jmedchem.1c00721] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The dysfunctional bromodomain PHD finger transcription factor (BPTF) exerts a pivotal influence in the occurrence and development of many human diseases, particularly cancers. Herein, through the structural decomposition of the reported BPTF inhibitor TP-238, the effective structural fragments were synthetically modified to obtain our lead compound DC-BPi-03. DC-BPi-03 was identified as a novel BPTF-BRD inhibitor with a moderate potency (IC50 = 698.3 ± 21.0 nM). A structure-guided structure-activity relationship exploration gave rise to two BPTF inhibitors with much higher affinities, DC-BPi-07 and DC-BPi-11. Notably, DC-BPi-07 and DC-BPi-11 show selectivities 100-fold higher than those of other BRD targets. The cocrystal structures of BPTF in complex with DC-BPi-07 and DC-BPi-11 demonstrate the rationale of chemical efforts from the atomic level. Further study showed that DC-BPi-11 significantly inhibited leukemia cell proliferation.
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Affiliation(s)
- Tian Lu
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.,Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou 550025, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China
| | - Haibo Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zhe Duan
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,School of Pharmacy, Nanchang University, Nanchang 330006, China
| | - Jun Wang
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jie Han
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Senhao Xiao
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - HuanHuan Chen
- Laboratory of Pharmaceutical Analysis, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Hao Jiang
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yu Chen
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Feng Yang
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qi Li
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Dongying Chen
- Laboratory of Pharmaceutical Analysis, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Jin Lin
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China
| | - Bo Li
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Hualiang Jiang
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Kaixian Chen
- School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China.,The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Wenchao Lu
- Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Hua Lin
- The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,Biomedical Research Center of South China, College of Life Sciences, Fujian Normal University, Fuzhou 350117, China
| | - Cheng Luo
- School of Pharmacy, Fujian Medical University, Fuzhou 350122, China.,School of Chinese Materia Medica, Nanjing University of Chinese Medicine, 138 Xianlin Road, Nanjing 210023, China.,School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China.,The Chemical Biology Center, Drug Design and Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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8
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Zahid H, Olson NM, Pomerantz WCK. Opportunity knocks for uncovering the new function of an understudied nucleosome remodeling complex member, the bromodomain PHD finger transcription factor, BPTF. Curr Opin Chem Biol 2021; 63:57-67. [PMID: 33706239 PMCID: PMC8384639 DOI: 10.1016/j.cbpa.2021.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 02/01/2021] [Indexed: 12/27/2022]
Abstract
Nucleosome remodeling provides access to genomic DNA for recruitment of the transcriptional machinery to mediate gene expression. The aberrant function of nucleosome remodeling complexes has been correlated to human cancer, making them emerging therapeutic targets. The bromodomain PHD finger transcription factor, BPTF, is the largest member of the human nucleosome remodeling factor NURF. Over the last five years, BPTF has become increasingly identified as a protumorigenic factor, prompting investigations into the molecular mechanisms associated with BPTF function. Despite a druggable bromodomain, small molecule discovery is at an early stage. Here we highlight recent investigations into the biology being discovered for BPTF, chemical biology approaches used to study its function, and small molecule inhibitors being designed as future chemical probes and therapeutics.
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Affiliation(s)
- Huda Zahid
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Noelle M Olson
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA
| | - William C K Pomerantz
- 207Pleasant St. SE, Department of Chemistry, University of Minnesota, Minneapolis, MN, 55455, USA.
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9
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Mélin L, Calosing C, Kharenko OA, Hansen HC, Gagnon A. Synthesis of NVS-BPTF-1 and evaluation of its biological activity. Bioorg Med Chem Lett 2021; 47:128208. [PMID: 34146702 DOI: 10.1016/j.bmcl.2021.128208] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/09/2021] [Accepted: 06/13/2021] [Indexed: 02/06/2023]
Abstract
BPTF (bromodomain and PHD finger containing transcription factor) is a multidomain protein that plays essential roles in transcriptional regulation, T-cell homeostasis and stem cell pluripotency. As part of the chromatin remodeling complex hNURF (nucleosome remodeling factor), BPTF epigenetic reader subunits are particularly important for BPTF cellular function. Here we report the synthesis of NVS-BPTF-1, a previously reported highly potent and selective BPTF-bromodomain inhibitor. Evaluation of the impact of the inhibition of BPTF-bromodomain using NVS-BPTF-1 on selected proteins involved in the antigen processing pathway revealed that exclusively targeting BPTF-bromodomain is insufficient to observe an increase of PSMB8, PSMB9, TAP1 and TAP2 proteins.
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Affiliation(s)
- Léa Mélin
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
| | - Cyrus Calosing
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Olesya A Kharenko
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Henrik C Hansen
- Zenith Epigenetics Ltd, Suite 300, 4820 Richard Road SW, Calgary, AB T3E 6L1, Canada
| | - Alexandre Gagnon
- Département de chimie, Université du Québec à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada.
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10
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Tyutyunyk-Massey L, Sun Y, Dao N, Ngo H, Dammalapati M, Vaidyanathan A, Singh M, Haqqani S, Haueis J, Finnegan R, Deng X, Kirberger SE, Bos PD, Bandyopadhyay D, Pomerantz WCK, Pommier Y, Gewirtz DA, Landry JW. Autophagy-Dependent Sensitization of Triple-Negative Breast Cancer Models to Topoisomerase II Poisons by Inhibition of the Nucleosome Remodeling Factor. Mol Cancer Res 2021; 19:1338-1349. [PMID: 33811160 DOI: 10.1158/1541-7786.mcr-20-0743] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 02/23/2021] [Accepted: 03/29/2021] [Indexed: 11/16/2022]
Abstract
Epigenetic regulators can modulate the effects of cancer therapeutics. To further these observations, we discovered that the bromodomain PHD finger transcription factor subunit (BPTF) of the nucleosome remodeling factor (NURF) promotes resistance to doxorubicin, etoposide, and paclitaxel in the 4T1 breast tumor cell line. BPTF functions in promoting resistance to doxorubicin and etoposide, but not paclitaxel, and may be selective to cancer cells, as a similar effect was not observed in embryonic stem cells. Sensitization to doxorubicin and etoposide with BPTF knockdown (KD) was associated with increased DNA damage, topoisomerase II (TOP2) crosslinking and autophagy; however, there was only a modest increase in apoptosis and no increase in senescence. Sensitization to doxorubicin was confirmed in vivo with the syngeneic 4T1 breast tumor model using both genetic and pharmacologic inhibition of BPTF. The effects of BPTF inhibition in vivo are autophagy dependent, based on genetic autophagy inhibition. Finally, treatment of 4T1, 66cl4, 4T07, MDA-MB-231, but not ER-positive 67NR and MCF7 breast cancer cells with the selective BPTF bromodomain inhibitor, AU1, recapitulates genetic BPTF inhibition, including in vitro sensitization to doxorubicin, increased TOP2-DNA crosslinks and DNA damage. Taken together, these studies demonstrate that BPTF provides resistance to the antitumor activity of TOP2 poisons, preventing the resolution of TOP2 crosslinking and associated autophagy. These studies suggest that BPTF can be targeted with small-molecule inhibitors to enhance the effectiveness of TOP2-targeted cancer chemotherapeutic drugs. IMPLICATIONS: These studies suggest NURF can be inhibited pharmacologically as a viable strategy to improve chemotherapy effectiveness.
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Affiliation(s)
- Liliya Tyutyunyk-Massey
- VCU Massey Cancer Center, Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Nga Dao
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Hannah Ngo
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Mallika Dammalapati
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Ashish Vaidyanathan
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Manjulata Singh
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Syed Haqqani
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Joshua Haueis
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Ryan Finnegan
- VCU Massey Cancer Center, Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Xiaoyan Deng
- VCU Massey Cancer Center, Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Steve E Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota
| | - Paula D Bos
- VCU Massey Cancer Center, Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Dipankar Bandyopadhyay
- VCU Massey Cancer Center, Department of Biostatistics, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | | | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NIH, Bethesda, Maryland
| | - David A Gewirtz
- VCU Massey Cancer Center, Department of Pharmacology and Toxicology, Virginia Commonwealth University School of Medicine, Richmond, Virginia
| | - Joseph W Landry
- VCU Massey Cancer Center, Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia.
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11
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Combined Protein- and Ligand-Observed NMR Workflow to Screen Fragment Cocktails against Multiple Proteins: A Case Study Using Bromodomains. Molecules 2020; 25:molecules25173949. [PMID: 32872491 PMCID: PMC7504435 DOI: 10.3390/molecules25173949] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
As fragment-based drug discovery has become mainstream, there has been an increase in various screening methodologies. Protein-observed 19F (PrOF) NMR and 1H CPMG NMR are two fragment screening assays that have complementary advantages. Here, we sought to combine these two NMR-based assays into a new screening workflow. This combination of protein- and ligand-observed experiments allows for a time- and resource-efficient multiplexed screen of mixtures of fragments and proteins. PrOF NMR is first used to screen mixtures against two proteins. Hit mixtures for each protein are identified then deconvoluted using 1H CPMG NMR. We demonstrate the benefit of this fragment screening method by conducting the first reported fragment screens against the bromodomains of BPTF and Plasmodium falciparum (Pf) GCN5 using 467 3D-enriched fragments. The hit rates were 6%, 5% and 4% for fragments binding BPTF, PfGCN5, and fragments binding both proteins, respectively. Select hits were characterized, revealing a broad range of affinities from low µM to mM dissociation constants. Follow-up experiments supported a low-affinity second binding site on PfGCN5. This approach can be used to bias fragment screens towards more selective hits at the onset of inhibitor development in a resource- and time-efficient manner.
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12
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Ycas PD, Zahid H, Chan A, Olson NM, Johnson JA, Talluri SK, Schonbrunn E, Pomerantz WCK. New inhibitors for the BPTF bromodomain enabled by structural biology and biophysical assay development. Org Biomol Chem 2020; 18:5174-5182. [PMID: 32588860 PMCID: PMC7393680 DOI: 10.1039/d0ob00506a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins regulate transcription through protein-protein interactions with chromatin and serve as scaffolding proteins for recruiting essential members of the transcriptional machinery. One such protein is the bromodomain and PHD-containing transcription factor (BPTF), the largest member of the nucleosome remodeling complex, NURF. Despite an emerging role for BPTF in regulating a diverse set of cancers, small molecule development for inhibiting the BPTF bromodomain has been lacking. Here we cross-validate three complementary biophysical assays to further the discovery of BPTF bromodomain inhibitors for chemical probe development: two direct binding assays (protein-observed 19F (PrOF) NMR and surface plasmon resonance (SPR)) and a competitive inhibition assay (AlphaScreen). We first compare the assays using three small molecules and acetylated histone peptides with reported affinity for the BPTF bromodomain. Using SPR with both unlabeled and fluorinated BPTF, we further determine that there is a minimal effect of 19F incorporation on ligand binding for future PrOF NMR experiments. To guide medicinal chemistry efforts towards chemical probe development, we subsequently evaluate two new BPTF inhibitor scaffolds with our suite of biophysical assays and rank-order compound affinities which could not otherwise be determined by PrOF NMR. Finally, we cocrystallize a subset of small molecule inhibitors and present the first published small molecule-protein structures with the BPTF bromodomain. We envision the biophysical assays described here and the structural insights from the crystallography will guide researchers towards developing selective and potent BPTF bromodomain inhibitors.
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Affiliation(s)
- Peter D Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - Noelle M Olson
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
| | - Siva K Talluri
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
| | - Ernst Schonbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, USA
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, USA.
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13
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Hall R, Dixon T, Dickson A. On Calculating Free Energy Differences Using Ensembles of Transition Paths. Front Mol Biosci 2020; 7:106. [PMID: 32582764 PMCID: PMC7291376 DOI: 10.3389/fmolb.2020.00106] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 05/06/2020] [Indexed: 12/30/2022] Open
Abstract
The free energy of a process is the fundamental quantity that determines its spontaneity or propensity at a given temperature. In particular, the binding free energy of a drug candidate to its biomolecular target is used as an objective quantity in drug design. Recently, binding kinetics—rates of association (kon) and dissociation (koff)—have also demonstrated utility for their ability to predict efficacy and in some cases have been shown to be more predictive than the binding free energy alone. Some methods exist to calculate binding kinetics from molecular simulations, although these are typically more difficult to calculate than the binding affinity as they depend on details of the transition path ensemble. Assessing these rate constants can be difficult, due to uncertainty in the definition of the bound and unbound states, large error bars and the lack of experimental data. As an additional consistency check, rate constants from simulation can be used to calculate free energies (using the log of their ratio) which can then be compared to free energies obtained experimentally or using alchemical free energy perturbation. However, in this calculation it is not straightforward to account for common, practical details such as the finite simulation volume or the particular definition of the “bound” and “unbound” states. Here we derive a set of correction terms that can be applied to calculations of binding free energies using full reactive trajectories. We apply these correction terms to revisit the calculation of binding free energies from rate constants for a host-guest system that was part of a blind prediction challenge, where significant deviations were observed between free energies calculated with rate ratios and those calculated from alchemical perturbation. The correction terms combine to significantly decrease the error with respect to computational benchmarks, from 3.4 to 0.76 kcal/mol. Although these terms were derived with weighted ensemble simulations in mind, some of the correction terms are generally applicable to free energies calculated using physical pathways via methods such as Markov state modeling, metadynamics, milestoning, or umbrella sampling.
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Affiliation(s)
- Robert Hall
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States
| | - Tom Dixon
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.,Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
| | - Alex Dickson
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI, United States.,Department of Computational Mathematics, Science and Engineering, Michigan State University, East Lansing, MI, United States
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14
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Olson NM, Kroc S, Johnson JA, Zahid H, Ycas PD, Chan A, Kimbrough JR, Kalra P, Schönbrunn E, Pomerantz WCK. NMR Analyses of Acetylated H2A.Z Isoforms Identify Differential Binding Interactions with the Bromodomain of the NURF Nucleosome Remodeling Complex. Biochemistry 2020; 59:1871-1880. [PMID: 32356653 DOI: 10.1021/acs.biochem.0c00159] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Gene specific recruitment of bromodomain-containing proteins to chromatin is affected by post-translational acetylation of lysine on histones. Whereas interactions of the bromodomain with acetylation patterns of native histones (H2A, H2B, H3, and H4) have been well characterized, the motif for recognition for histone variants H2A.Z I and H2A.Z II by bromodomains has yet to be fully investigated. Elucidating these molecular mechanisms is crucial for understanding transcriptional regulation in cellular processes involved in both development and disease. Here, we have used protein-observed fluorine NMR to fully characterize the affinities of H2A.Z I and II acetylation patterns for BPTF's bromodomain and found the diacetylated mark of lysine 7 and 13 on H2A.Z II to have the strongest interaction with K7ac preferentially engaging the binding site. We further examined the selectivity of H2A.Z histones against a variety of bromodomains, revealing that the bromodomain of CECR2 binds with the highest affinity and specificity for acetylated H2A.Z I over isoform II. These results support a possible role for different H2A.Z transcriptional activation mechanisms that involve recruitment of chromatin remodeling complexes.
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Affiliation(s)
- Noelle M Olson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Samantha Kroc
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Jorden A Johnson
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Peter D Ycas
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Jennifer R Kimbrough
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455, United States
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15
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McEvoy CR, Fox SB, Prall OWJ. Emerging entities in NUTM1-rearranged neoplasms. Genes Chromosomes Cancer 2020; 59:375-385. [PMID: 32060986 DOI: 10.1002/gcc.22838] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 12/11/2022] Open
Abstract
Structural alterations of NUTM1 were originally thought to be restricted to poorly differentiated carcinomas with variable squamous differentiation originating in the midline organs of children and adolescents. Termed NUT carcinomas (NCs), they were defined by a t(15;19) chromosomal rearrangement that was found to result in a BRD4-NUTM1 gene fusion. However, the use of DNA and RNA-based next-generation sequencing has recently revealed a multitude of new NUTM1 fusion partners in a diverse array of neoplasms including sarcoma-like tumors, poromas, and acute lymphoblastic leukemias (ALLs) that we propose to call NUTM1-rearranged neoplasms (NRNs). Intriguingly, the nosology of NRNs often correlates with the functional classification of the fusion partner, suggesting different oncogenic mechanisms within each NRN division. Indeed, whereas NCs are characterized by their aggressiveness and intransigence to standard therapeutic measures, the more positive clinical outcomes seen in some sarcoma and ALL NRNs may reflect these mechanistic differences. Here we provide a broad overview of the molecular, nosological, and clinical features in these newly discovered neoplastic entities. We describe how aberrant expression of NUTM1 due to fusion with an N-terminal DNA/chromatin-binding protein can generate a potentially powerful chromatin modifier that can give rise to oncogenic transformation in numerous cellular contexts. We also conclude that classification, clinical behavior, and therapeutic options may be best defined by the NUTM1 fusion partner rather than by tumor morphology or immunohistochemical profile.
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Affiliation(s)
- Christopher R McEvoy
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Owen W J Prall
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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16
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Nguyen HHT, Yeoh LM, Chisholm SA, Duffy MF. Developments in drug design strategies for bromodomain protein inhibitors to target Plasmodium falciparum parasites. Expert Opin Drug Discov 2019; 15:415-425. [PMID: 31870185 DOI: 10.1080/17460441.2020.1704251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Bromodomains (BRDs) bind to acetylated lysine residues, often on histones. The BRD proteins can contribute to gene regulation either directly through enzymatic activity or indirectly through recruitment of chromatin-modifying complexes or transcription factors. There is no evidence of direct orthologues of the Plasmodium falciparum BRD proteins (PfBDPs) outside the apicomplexans. PfBDPs are expressed during the parasite's life cycle in both the human host's blood and in the mosquito. PfBDPs could also prove to be promising targets for novel antimalarials, which are urgently required to address increasing drug resistance.Areas covered: This review discusses recent studies of the biology of PfBDPs, current target-based strategies for PfBDP inhibitor discovery, and different approaches to the important step of validating the specificity of hit compounds for PfBDPs.Expert opinion: The novelty of Plasmodium BRDs suggests that they could be targeted by selective compounds. Chemical series that showed promise in screens against human BRDs could be leveraged to create targeted compound libraries, as could hits from P. falciparum phenotypic screens. These targeted libraries and hits could be screened in target-based strategies aimed at discovery and optimization of novel inhibitors of PfBDPs. A key task for the field is to generate parasite assays to validate the hit compounds' specificity for PfBDPs.
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Affiliation(s)
- Hanh H T Nguyen
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Lee M Yeoh
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Scott A Chisholm
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Michael F Duffy
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
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17
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Abstract
Inhibitor discovery for protein-protein interactions has proven difficult due to the large protein surface areas and dynamic interfaces involved. This is particularly the case when targeting transcription-factor-protein interactions. To address this challenge, structural biology approaches for ligand discovery using X-ray crystallography, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy have had a significant impact on advancing small molecule inhibitors into the clinic, including the U.S. Food and Drug Administration approved drug, Venetoclax. Inspired by the protein-observed NMR approach using 1H-15N-HSQC NMR which detects chemical shift perturbations of 15N-labeled amides, we have applied a complementary protein-observed 19F NMR approach using 19F-labeled side-chains that are enriched at protein-protein-interaction interfaces. This protein-observed 19F NMR assay is abbreviated PrOF NMR to distinguish the experiment from the more commonly employed ligand-observed 19F NMR methods. In this Account, we describe our efforts using PrOF NMR as a ligand discovery tool, particularly for fragment-based ligand discovery (FBLD). We metabolically label the aromatic amino acids on proteins due to the enrichment of aromatic residues at protein interfaces. We choose the 19F nucleus due to its high signal sensitivity and the hyperresponsiveness of 19F to changes in chemical environment. Simultaneous labeling with two different types of fluorinated aromatic amino acids for PrOF NMR has also been achieved. We first describe the technical aspects of considering the application of PrOF NMR for characterizing native protein-protein interactions and for ligand screening. Several test cases are further described with a focus on a transcription factor coactivator interaction with the KIX domain of CBP/p300 and two epigenetic regulatory domains, the bromodomains of BRD4 and BPTF. Through these case studies, we highlight medicinal chemistry applications in FBLD, selectivity screens, structure-activity relationship (SAR) studies, and ligand deconstruction approaches. These studies have led to the discovery of some of the first inhibitors for BPTF and a novel inhibitor class for the N-terminal bromodomain of BRD4. The speed, ease of interpretation, and relatively low concentration of protein needed for NMR-based binding experiments affords a rapid, structural biology-based method to discover and characterize both native and new ligands for bromodomains, and it may find utility in the study of additional epigenetic proteins and transcription-factor-protein interactions.
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Affiliation(s)
- Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St. SE, Minneapolis, Minnesota 55455, United States
| | - Steven E. Kirberger
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
| | - William C. K. Pomerantz
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St. SE, Minneapolis, Minnesota 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455, United States
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18
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Johnson JA, Nicolaou CA, Kirberger SE, Pandey AK, Hu H, Pomerantz WCK. Evaluating the Advantages of Using 3D-Enriched Fragments for Targeting BET Bromodomains. ACS Med Chem Lett 2019; 10:1648-1654. [PMID: 31857841 DOI: 10.1021/acsmedchemlett.9b00414] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 11/22/2019] [Indexed: 02/08/2023] Open
Abstract
Fragment-based ligand discovery has been successful in targeting diverse proteins. Despite drug-like molecules having more 3D character, traditional fragment libraries are largely composed of flat, aromatic fragments. The use of 3D-enriched fragments for enhancing library diversity is underexplored especially against protein-protein interactions. Here, we evaluate using 3D-enriched fragments against bromodomains. Bromodomains are highly ligandable, but selectivity remains challenging, particularly for bromodomain and extraterminal (BET) family bromodomains. We screened a 3D-enriched fragment library against BRD4(D1) via 1H CPMG NMR with a protein-observed 19F NMR secondary assay. The screen led to 29% of the hits that are selective over two related bromodomains, BRDT(D1) and BPTF, and the identification of underrepresented chemical bromodomain inhibitor scaffolds. Initial structure-activity relationship studies guided by X-ray crystallography led to a ligand-efficient thiazepane, with good selectivity and affinity for BET bromodomains. These results suggest that the incorporation of 3D-enriched fragments to increase library diversity can benefit bromodomain screening.
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Affiliation(s)
- Jorden A. Johnson
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christos A. Nicolaou
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - Steven E. Kirberger
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Anil K. Pandey
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Haitao Hu
- Discovery Chemistry Research & Technologies, Lilly Research Laboratories, Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285, United States
| | - William C. K. Pomerantz
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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