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Taylor SJ, Stauber J, Bohorquez O, Tatsumi G, Kumari R, Chakraborty J, Bartholdy BA, Schwenger E, Sundaravel S, Farahat AA, Wheat JC, Goldfinger M, Verma A, Kumar A, Boykin DW, Stengel KR, Poon GMK, Steidl U. Pharmacological restriction of genomic binding sites redirects PU.1 pioneer transcription factor activity. Nat Genet 2024:10.1038/s41588-024-01911-7. [PMID: 39294495 DOI: 10.1038/s41588-024-01911-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 08/14/2024] [Indexed: 09/20/2024]
Abstract
Transcription factor (TF) DNA-binding dynamics govern cell fate and identity. However, our ability to pharmacologically control TF localization is limited. Here we leverage chemically driven binding site restriction leading to robust and DNA-sequence-specific redistribution of PU.1, a pioneer TF pertinent to many hematopoietic malignancies. Through an innovative technique, 'CLICK-on-CUT&Tag', we characterize the hierarchy of de novo PU.1 motifs, predicting occupancy in the PU.1 cistrome under binding site restriction. Temporal and single-molecule studies of binding site restriction uncover the pioneering dynamics of native PU.1 and identify the paradoxical activation of an alternate target gene set driven by PU.1 localization to second-tier binding sites. These transcriptional changes were corroborated by genetic blockade and site-specific reporter assays. Binding site restriction and subsequent PU.1 network rewiring causes primary human leukemia cells to differentiate. In summary, pharmacologically induced TF redistribution can be harnessed to govern TF localization, actuate alternate gene networks and direct cell fate.
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Affiliation(s)
- Samuel J Taylor
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jacob Stauber
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Oliver Bohorquez
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Goichi Tatsumi
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rajni Kumari
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Joyeeta Chakraborty
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Emily Schwenger
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sriram Sundaravel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Abdelbasset A Farahat
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Master of Pharmaceutical Sciences Program, California Northstate University, Elk Grove, CA, USA
| | - Justin C Wheat
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Mendel Goldfinger
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
| | - Amit Verma
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
- Department of Medicine, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Kristy R Stengel
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Oncology, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Blood Cancer Institute, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Montefiore Einstein Comprehensive Cancer Center, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
- Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Albert Einstein College of Medicine, Bronx, NY, USA.
- Department of Medicine, Albert Einstein College of Medicine - Montefiore Medical Center, Bronx, NY, USA.
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Chemical restriction of PU.1 genomic binding sites activates alternate gene networks. Nat Genet 2024:10.1038/s41588-024-01912-6. [PMID: 39294498 DOI: 10.1038/s41588-024-01912-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
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Ogbonna EN, Terrell JR, Paul A, Farahat AA, Poon GMK, Boykin DW, Wilson WD. Single GC base pair recognition by a heterocyclic diamidine: structures, affinities, and dynamics. RSC Adv 2024; 14:29675-29682. [PMID: 39297050 PMCID: PMC11408989 DOI: 10.1039/d4ra05957c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Accepted: 09/04/2024] [Indexed: 09/21/2024] Open
Abstract
The recognition of specific genomic arrangements by rationally designed small molecules is fundamental for the expansion of targeted gene expression. Here, we report the first X-ray crystal structures that demonstrate single G (guanine) recognition by a highly selective diamidine (DB2447) in a mixed DNA sequence. The study presents detailed structural information on the mechanism of single G recognition by D2447 and its various interactions in the DNA minor groove. Molecular dynamics and binding studies were used to evaluate the details of our reported structures. The study provides structural insight and resources necessary for understanding single G selection in genomic sequences.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
| | - J Ross Terrell
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
| | - Ananya Paul
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
- Master of Pharmaceutical Science Program, California North State University Elk Grove CA 95757 USA
| | - Gregory M K Poon
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
| | - David W Boykin
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
| | - W David Wilson
- Department of Chemistry and Centre of Diagnostics and Therapeutics, Georgia State University Atlanta GA 30303-3083 USA +1 404-413-5505 +1 404-413-5503
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Shi Y, Zheng M, Luo Y, Li J, Ouyang F, Zhao Y, Wang J, Ma Z, Meng C, Bi Y, Cheng L, Jing J. Targeting transcription factor pu.1 for improving neurologic outcomes after spinal cord injury. Front Neurosci 2024; 18:1418615. [PMID: 39211434 PMCID: PMC11358095 DOI: 10.3389/fnins.2024.1418615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Accepted: 06/10/2024] [Indexed: 09/04/2024] Open
Abstract
Background After spinal cord injury (SCI), lipid metabolism dysregulation at the lesion site exacerbates secondary damage. The transcription factor pu.1 has been implicated as a negative regulator of multiple lipid metabolism-related genes and pathways. However, its role in post-SCI lipid metabolism remains unclear. Methods We employed a mouse model of complete T10 crush SCI. Non-targeted metabolomics and bioinformatics analysis were utilized to investigate lipid metabolism at the lesion site after SCI. Polarized light imaging was used to evaluate the presence of cholesterol crystals. DB1976, a specific inhibitor of pu.1, was administered to examine its impact on local lipid metabolism after SCI. Immunofluorescence staining was performed to assess pu.1 expression and distribution, and to evaluate lipid droplet formation, astrocytic/fibrotic scar development, inflammatory cell infiltration, and tight junctions within the vasculature. Results Non-targeted metabolomics and bioinformatics analyses revealed significant alterations in lipid metabolism components after SCI. Moreover, immunofluorescence staining and polarized light imaging demonstrated substantial BODIPY+ lipid droplet accumulation and persistent cholesterol crystal formation at the lesion site after SCI. Increased pu.1 expression was predominantly observed within macrophages/microglia at the lesion site after SCI. DB1976 treatment significantly mitigated lipid droplet accumulation and cholesterol crystal formation, reduced CD68+ macrophage/microglial infiltration, and attenuated fibrotic scar formation. Moreover, DB1976 treatment promoted the expression of claudin-5 and zonula occludens-1 between vascular endothelial cells and enhanced GFAP+ glial connectivity after SCI. Conclusion Our study reveals a significant correlation between lipid metabolism disturbance post-SCI and transcription factor pu.1 upregulation, specifically in macrophages/microglia at the lesion site. Thus, targeted pu.1 modulation has the potential to yield promising results by substantially diminishing the deposition of lipid metabolism byproducts at the lesion site and fostering a milieu conducive to SCI repair.
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Affiliation(s)
- Yi Shi
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Meige Zheng
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yang Luo
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jianjian Li
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Fangru Ouyang
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanzhe Zhao
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jingwen Wang
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zhida Ma
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Congpeng Meng
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yihui Bi
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li Cheng
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Juehua Jing
- Department of Orthopedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopedics, Research Center for Translational Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
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Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. Nat Commun 2024; 15:5514. [PMID: 38951492 PMCID: PMC11217462 DOI: 10.1038/s41467-024-49635-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
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Affiliation(s)
- Maria C Virgilio
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Barkha Ramnani
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Thomas Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
| | - W Miguel Disbennett
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- Post-Baccalaureate Research Education Program (PREP), University of Michigan, Ann Arbor, MI, USA
- University of Pennsylvania, Philadelphia, PA, USA
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA
- ImmunoVec, Inc., Los Angeles, CA, USA
| | - Joshua D Welch
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
- Department of Computer Science and Engineering, University of Michigan, Ann Arbor, USA
| | - Kathleen L Collins
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA.
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA.
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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6
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Karpurapu M, Kakarala KK, Chung S, Nie Y, Koley A, Dougherty P, Christman JW. Epigallocatechin gallate regulates the myeloid-specific transcription factor PU.1 in macrophages. PLoS One 2024; 19:e0301904. [PMID: 38662666 PMCID: PMC11045095 DOI: 10.1371/journal.pone.0301904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Our previous research demonstrated that PU.1 regulates expression of the genes involved in inflammation in macrophages. Selective knockdown of PU.1 in macrophages ameliorated LPS-induced acute lung injury (ALI) in bone marrow chimera mice. Inhibitors that block the transcriptional activity of PU.1 in macrophages have the potential to mitigate the pathophysiology of LPS-induced ALI. However, complete inactivation of PU.1 gene disrupts normal myelopoiesis. Although the green tea polyphenol Epigallocatechin gallate (EGCG) has been shown to regulate inflammatory genes in various cell types, it is not known if EGCG alters the transcriptional activity of PU.1 protein. Using Schrodinger Glide docking, we have identified that EGCG binds with PU.1 protein, altering its DNA-binding and self-dimerization activity. In silico analysis shows that EGCG forms Hydrogen bonds with Glutamic Acid 209, Leucine 250 in DNA binding and Lysine 196, Tryptophan 193, and Leucine 182 in the self-dimerization domain of the PU.1 protein. Experimental validation using mouse bone marrow-derived macrophages (BMDM) confirmed that EGCG inhibits both DNA binding by PU.1 and self-dimerization. Importantly, EGCG had no impact on expression of the total PU.1 protein levels but significantly reduced expression of various inflammatory genes and generation of ROS. In summary, we report that EGCG acts as an inhibitor of the PU.1 transcription factor in macrophages.
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Affiliation(s)
- Manjula Karpurapu
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | | | - Sangwoon Chung
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - Yunjuan Nie
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
- Department of Basic Medicine, Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, 214122, P.R. China
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - Patrick Dougherty
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, United States of America
| | - John W. Christman
- Division of Pulmonary, Davis Heart and Lung Research Institute, Critical Care and Sleep Medicine, Ohio State University Wexner Medical Center, Columbus, OH, United States of America
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7
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Virgilio MC, Ramnani B, Chen T, Disbennett WM, Lubow J, Welch JD, Collins KL. HIV-1 Vpr combats the PU.1-driven antiviral response in primary human macrophages. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.21.533528. [PMID: 36993393 PMCID: PMC10055223 DOI: 10.1101/2023.03.21.533528] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
HIV-1 Vpr promotes efficient spread of HIV-1 from macrophages to T cells by transcriptionally downmodulating restriction factors that target HIV-1 Envelope protein (Env). Here we find that Vpr induces broad transcriptomic changes by targeting PU.1, a transcription factor necessary for expression of host innate immune response genes, including those that target Env. Consistent with this, we find silencing PU.1 in infected macrophages lacking Vpr rescues Env. Vpr downmodulates PU.1 through a proteasomal degradation pathway that depends on physical interactions with PU.1 and DCAF1, a component of the Cul4A E3 ubiquitin ligase. The capacity for Vpr to target PU.1 is highly conserved across primate lentiviruses. In addition to impacting infected cells, we find that Vpr suppresses expression of innate immune response genes in uninfected bystander cells, and that virion-associated Vpr can degrade PU.1. Together, we demonstrate Vpr counteracts PU.1 in macrophages to blunt antiviral immune responses and promote viral spread.
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8
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Patalano SD, Fuxman Bass P, Fuxman Bass JI. Transcription factors in the development and treatment of immune disorders. Transcription 2023:1-23. [PMID: 38100543 DOI: 10.1080/21541264.2023.2294623] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 12/08/2023] [Indexed: 12/17/2023] Open
Abstract
Immune function is highly controlled at the transcriptional level by the binding of transcription factors (TFs) to promoter and enhancer elements. Several TF families play major roles in immune gene expression, including NF-κB, STAT, IRF, AP-1, NRs, and NFAT, which trigger anti-pathogen responses, promote cell differentiation, and maintain immune system homeostasis. Aberrant expression, activation, or sequence of isoforms and variants of these TFs can result in autoimmune and inflammatory diseases as well as hematological and solid tumor cancers. For this reason, TFs have become attractive drug targets, even though most were previously deemed "undruggable" due to their lack of small molecule binding pockets and the presence of intrinsically disordered regions. However, several aspects of TF structure and function can be targeted for therapeutic intervention, such as ligand-binding domains, protein-protein interactions between TFs and with cofactors, TF-DNA binding, TF stability, upstream signaling pathways, and TF expression. In this review, we provide an overview of each of the important TF families, how they function in immunity, and some related diseases they are involved in. Additionally, we discuss the ways of targeting TFs with drugs along with recent research developments in these areas and their clinical applications, followed by the advantages and disadvantages of targeting TFs for the treatment of immune disorders.
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Affiliation(s)
- Samantha D Patalano
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
| | - Paula Fuxman Bass
- Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Juan I Fuxman Bass
- Biology Department, Boston University, Boston, MA, USA
- Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
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9
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Ralvenius WT, Mungenast AE, Woolf H, Huston MM, Gillingham TZ, Godin SK, Penney J, Cam HP, Gao F, Fernandez CG, Czako B, Lightfoot Y, Ray WJ, Beckmann A, Goate AM, Marcora E, Romero-Molina C, Ayata P, Schaefer A, Gjoneska E, Tsai LH. A novel molecular class that recruits HDAC/MECP2 complexes to PU.1 motifs reduces neuroinflammation. J Exp Med 2023; 220:e20222105. [PMID: 37642942 PMCID: PMC10465325 DOI: 10.1084/jem.20222105] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/26/2023] [Accepted: 07/27/2023] [Indexed: 08/31/2023] Open
Abstract
Pervasive neuroinflammation occurs in many neurodegenerative diseases, including Alzheimer's disease (AD). SPI1/PU.1 is a transcription factor located at a genome-wide significant AD-risk locus and its reduced expression is associated with delayed onset of AD. We analyzed single-cell transcriptomic datasets from microglia of human AD patients and found an enrichment of PU.1-binding motifs in the differentially expressed genes. In hippocampal tissues from transgenic mice with neurodegeneration, we found vastly increased genomic PU.1 binding. We then screened for PU.1 inhibitors using a PU.1 reporter cell line and discovered A11, a molecule with anti-inflammatory efficacy and nanomolar potency. A11 regulated genes putatively by recruiting a repressive complex containing MECP2, HDAC1, SIN3A, and DNMT3A to PU.1 motifs, thus representing a novel mechanism and class of molecules. In mouse models of AD, A11 ameliorated neuroinflammation, loss of neuronal integrity, AD pathology, and improved cognitive performance. This study uncovers a novel class of anti-inflammatory molecules with therapeutic potential for neurodegenerative disorders.
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Affiliation(s)
- William T. Ralvenius
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Alison E. Mungenast
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hannah Woolf
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Margaret M. Huston
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Tyler Z. Gillingham
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stephen K. Godin
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jay Penney
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Hugh P. Cam
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Fan Gao
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Celia G. Fernandez
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Barbara Czako
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yaima Lightfoot
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - William J. Ray
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Adrian Beckmann
- The Neurodegeneration Consortium, Therapeutics Discovery Division, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Alison M. Goate
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Edoardo Marcora
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Carmen Romero-Molina
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pinar Ayata
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Advanced Science Research Center at the Graduate Center, Neuroscience Initiative, City University of New York, New York, NY, USA
| | - Anne Schaefer
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Max Planck Institute for Biology of Ageing, Cologne, Germany
| | - Elizabeta Gjoneska
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Neurobiology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, NC, USA
| | - Li-Huei Tsai
- Department of Brain and Cognitive Sciences, Picower Institute for Learning and Memory, Massachusetts Institute of Technology, Cambridge, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
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10
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Zhang ZJ, Wu QF, Ren AQ, Chen Q, Shi JZ, Li JP, Liu XY, Zhang ZJ, Tang YZ, Zhao Y, Yao NN, Zhang XY, Liu CP, Dong G, Zhao JX, Xu MJ, Yue YQ, Hu J, Sun F, Liu Y, Ao QL, Zhou FL, Wu H, Zhang TC, Zhu HC. ATF4 renders human T-cell acute lymphoblastic leukemia cell resistance to FGFR1 inhibitors through amino acid metabolic reprogramming. Acta Pharmacol Sin 2023; 44:2282-2295. [PMID: 37280363 PMCID: PMC10618259 DOI: 10.1038/s41401-023-01108-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/09/2023] [Indexed: 06/08/2023] Open
Abstract
Abnormalities of FGFR1 have been reported in multiple malignancies, suggesting FGFR1 as a potential target for precision treatment, but drug resistance remains a formidable obstacle. In this study, we explored whether FGFR1 acted a therapeutic target in human T-cell acute lymphoblastic leukemia (T-ALL) and the molecular mechanisms underlying T-ALL cell resistance to FGFR1 inhibitors. We showed that FGFR1 was significantly upregulated in human T-ALL and inversely correlated with the prognosis of patients. Knockdown of FGFR1 suppressed T-ALL growth and progression both in vitro and in vivo. However, the T-ALL cells were resistant to FGFR1 inhibitors AZD4547 and PD-166866 even though FGFR1 signaling was specifically inhibited in the early stage. Mechanistically, we found that FGFR1 inhibitors markedly increased the expression of ATF4, which was a major initiator for T-ALL resistance to FGFR1 inhibitors. We further revealed that FGFR1 inhibitors induced expression of ATF4 through enhancing chromatin accessibility combined with translational activation via the GCN2-eIF2α pathway. Subsequently, ATF4 remodeled the amino acid metabolism by stimulating the expression of multiple metabolic genes ASNS, ASS1, PHGDH and SLC1A5, maintaining the activation of mTORC1, which contributed to the drug resistance in T-ALL cells. Targeting FGFR1 and mTOR exhibited synergistically anti-leukemic efficacy. These results reveal that FGFR1 is a potential therapeutic target in human T-ALL, and ATF4-mediated amino acid metabolic reprogramming contributes to the FGFR1 inhibitor resistance. Synergistically inhibiting FGFR1 and mTOR can overcome this obstacle in T-ALL therapy.
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Affiliation(s)
- Zi-Jian Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qi-Fang Wu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - An-Qi Ren
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qian Chen
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jiang-Zhou Shi
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jia-Peng Li
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
- School of Science, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Xi-Yu Liu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Zhi-Jie Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yu-Zhe Tang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yuan Zhao
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Ning-Ning Yao
- Peking-Tsinghua Center for Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Xiao-Yu Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Chang-Peng Liu
- Department of Medical Records, Office for DRGs (Diagnosis Related Groups), Henan Cancer Hospital, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450003, China
| | - Ge Dong
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jia-Xuan Zhao
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education & Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China
| | - Mei-Jun Xu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yun-Qiang Yue
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jia Hu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Fan Sun
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Yu Liu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qi-Lin Ao
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
- Department of Pathology, School of Basic Medical Science, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Fu-Ling Zhou
- Department of Hematology, Zhongnan Hospital of Wuhan University, Wuhan, 430071, China
| | - Hong Wu
- Peking-Tsinghua Center for Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Tong-Cun Zhang
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China.
- Key Lab of Industrial Fermentation Microbiology of the Ministry of Education & Tianjin Key Lab of Industrial Microbiology, College of Biotechnology, Tianjin University of Science and Technology, Tianjin, 300457, China.
| | - Hai-Chuan Zhu
- Institute of Biology and Medicine, College of Life and Health Sciences, Wuhan University of Science and Technology, Wuhan, 430065, China.
- College of Life Science, Wuchang University of Technology, Wuhan, 430223, China.
- Synergy Innovation Center of Biological Peptide Antidiabetics of Hubei Province, College of Life Science, Wuchang University of Technology, Wuhan, 430223, China.
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11
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Ogbonna E, Paul A, Farahat AA, Terrell JR, Mineva E, Ogbonna V, Boykin DW, Wilson WD. X-ray Structure Characterization of the Selective Recognition of AT Base Pair Sequences. ACS BIO & MED CHEM AU 2023; 3:335-348. [PMID: 37599788 PMCID: PMC10436263 DOI: 10.1021/acsbiomedchemau.3c00002] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/23/2023] [Accepted: 03/24/2023] [Indexed: 08/22/2023]
Abstract
The rational design of small molecules that target specific DNA sequences is a promising strategy to modulate gene expression. This report focuses on a diamidinobenzimidazole compound, whose selective binding to the minor groove of AT DNA sequences holds broad significance in the molecular recognition of AT-rich human promoter sequences. The objective of this study is to provide a more detailed and systematized understanding, at an atomic level, of the molecular recognition mechanism of different AT-specific sequences by a rationally designed minor groove binder. The specialized method of X-ray crystallography was utilized to investigate how the sequence-dependent recognition properties in general, A-tract, and alternating AT sequences affect the binding of diamidinobenzimidazole in the DNA minor groove. While general and A-tract AT sequences give a narrower minor groove, the alternating AT sequences intrinsically have a wider minor groove which typically constricts upon binding. A strong and direct hydrogen bond between the N-H of the benzimidazole and an H-bond acceptor atom in the minor groove is essential for DNA recognition in all sequences described. In addition, the diamidine compound specifically utilizes an interfacial water molecule for its DNA binding. DNA complexes of AATT and AAAAAA recognition sites show that the diamidine compound can bind in two possible orientations with a preference for water-assisted hydrogen bonding at either cationic end. The complex structures of AAATTT, ATAT, ATATAT, and AAAA are bound in a singular orientation. Analysis of the helical parameters shows a minor groove expansion of about 1 Å across all the nonalternating DNA complexes. The results from this systematic approach will convey a greater understanding of the specific recognition of a diverse array of AT-rich sequences by small molecules and more insight into the design of small molecules with enhanced specificity to AT and mixed DNA sequences.
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Affiliation(s)
- Edwin
N. Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ananya Paul
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Abdelbasset A. Farahat
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
- Department
of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Master
of Pharmaceutical Sciences Program, California
North State University, 9700 W Taron Dr., Elk Grove, California 95757, United States
| | - J. Ross Terrell
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Ekaterina Mineva
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - Victor Ogbonna
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - David W Boykin
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
| | - W. David Wilson
- Department
of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia 30303-3083, United States
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12
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Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK. DNA selection by the master transcription factor PU.1. Cell Rep 2023; 42:112671. [PMID: 37352101 PMCID: PMC10479921 DOI: 10.1016/j.celrep.2023.112671] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/07/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
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Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Samuel J Taylor
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yue Lu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Ulrich Steidl
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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13
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Farahat AA, Kumar A, Wenzler T, Brun R, Paul A, Guo P, Wilson WD, Boykin DW. Investigation of the effect of structure modification of furamidine on the DNA minor groove binding and antiprotozoal activity. Eur J Med Chem 2023; 252:115287. [PMID: 36958267 PMCID: PMC10127280 DOI: 10.1016/j.ejmech.2023.115287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/05/2023] [Accepted: 03/14/2023] [Indexed: 03/25/2023]
Abstract
New analogs of the antiprotozoal agent Furamidine were prepared utilizing Stille coupling reactions and amidation of the bisnitrile intermediate using lithium bis-trimethylsilylamide. Both the phenyl groups and the furan moiety of furamidine were replaced by heterocycles including thiophene, selenophene, indole or benzimidazole. Based upon the ΔTm and the CD results, the new compounds showed strong binding to the DNA minor groove. The new analogues are also more active both in vitro and in vivo than furamidine. Compounds 7a, 7b, and 7f showed the highest activity in vivo by curing 75% of animals, and this merits further evaluation.
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Affiliation(s)
- Abdelbasset A Farahat
- Masters of Pharmaceutical Sciences Program, California Northstate University, Elk Grove, CA, 95757, USA; Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, 35516, Egypt.
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Tanja Wenzler
- Swiss Tropical and Public Health Institute, Basel, 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Reto Brun
- Swiss Tropical and Public Health Institute, Basel, 4002, Switzerland; University of Basel, Basel, 4003, Switzerland
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Pu Guo
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
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14
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Zhang LY, Tan Y, Luo XJ, Wu JF, Ni YR. The roles of ETS transcription factors in liver fibrosis. Hum Cell 2023; 36:528-539. [PMID: 36547849 DOI: 10.1007/s13577-022-00848-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
E26 transformation specific or E twenty-six (ETS) protein family consists of 28 transcription factors, five of which, named ETS1/2, PU.1, ERG and EHF, are known to involve in the development of liver fibrosis, and are expected to become diagnostic markers or therapeutic targets of liver fibrosis. In recent years, some small molecule inhibitors of ETS protein family have been discovered, which might open up a new path for the liver fibrosis therapy targeting ETS. This article reviews the research progress of ETS family members in the development liver fibrosis as well as their prospect of clinical application.
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Affiliation(s)
- Li-Ye Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Yong Tan
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Xiao-Jie Luo
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Jiang-Feng Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
| | - Yi-Ran Ni
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
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15
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Vijayaraj A, Prabu R, Suresh R, Sangeetha Kumari R, Kaviyarasan V, Narayanan V, Tamizhdurai P, Mangesh V, Ali Alasmary F, Rajaji U, Govindasamy M. DNA binding, Cleavage, Catalytic, Magnetic Active; 2,2–bipyridyl based d-f hetero binuclear Gd(III), Cu(II) Complexes and Their Electrochemical, Fluorescence Studies. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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16
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Ogbonna EN, Paul A, Ross Terrell J, Fang Z, Chen C, Poon GMK, Boykin DW, Wilson WD. Drug design and DNA structural research inspired by the Neidle laboratory: DNA minor groove binding and transcription factor inhibition by thiophene diamidines. Bioorg Med Chem 2022; 68:116861. [PMID: 35661929 PMCID: PMC9707304 DOI: 10.1016/j.bmc.2022.116861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/23/2022] [Accepted: 05/26/2022] [Indexed: 11/02/2022]
Abstract
The understanding of sequence-specific DNA minor groove interactions has recently made major steps forward and as a result, the goal of development of compounds that target the minor groove is an active research area. In an effort to develop biologically active minor groove agents, we are preparing and exploring the DNA interactions of diverse diamidine derivatives with a 5'-GAATTC-3' binding site using a powerful array of methods including, biosensor-SPR methods, and X-ray crystallography. The benzimidazole-thiophene module provides an excellent minor groove recognition component. A central thiophene in a benzimidazole-thiophene-phenyl aromatic system provides essentially optimum curvature for matching the shape of the minor groove. Comparison of that structure to one with the benzimidazole replaced with an indole shows that the two structures are very similar, but have some interesting and important differences in electrostatic potential maps, the DNA minor groove binding structure based on x-ray crystallographic analysis, and inhibition of the major groove binding PU.1 transcription factor complex. The binding KD for both compounds is under 10 nM and both form amidine H-bonds to DNA bases. They both have bifurcated H-bonds from the benzimidazole or indole groups to bases at the center of the -AATT- binding site. Analysis of the comparative results provides an excellent understanding of how thiophene compounds recognize the minor groove and can act as transcription factor inhibitors.
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Affiliation(s)
- Edwin N Ogbonna
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - J Ross Terrell
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ziyuan Fang
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Cen Chen
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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17
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Paul A, Farahat AA, Boykin DW, Wilson WD. Thermodynamic Factors That Drive Sequence-Specific DNA Binding of Designed, Synthetic Minor Groove Binding Agents. Life (Basel) 2022; 12:life12050681. [PMID: 35629349 PMCID: PMC9147024 DOI: 10.3390/life12050681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/29/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Ken Breslauer began studies on the thermodynamics of small cationic molecules binding in the DNA minor groove over 30 years ago, and the studies reported here are an extension of those ground-breaking reports. The goals of this report are to develop a detailed understanding of the binding thermodynamics of pyridine-based sequence-specific minor groove binders that have different terminal cationic groups. We apply biosensor-surface plasmon resonance and ITC methods to extend the understanding of minor groove binders in two directions: (i) by using designed, heterocyclic dicationic minor groove binders that can incorporate a G•C base pair (bp), with flanking AT base pairs, into their DNA recognition site, and bind to DNA sequences specifically; and (ii) by using a range of flanking AT sequences to better define molecular recognition of the minor groove. A G•C bp in the DNA recognition site causes a generally more negative binding enthalpy than with most previously used pure AT binding sites. The binding is enthalpy-driven at 25 °C and above. The flanking AT sequences also have a large effect on the binding energetics with the -AAAGTTT- site having the strongest affinity. As a result of these studies, we now have a much better understanding of the effects of the DNA sequence and compound structure on the molecular recognition and thermodynamics of minor groove complexes.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
| | - Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA; (A.P.); (A.A.F.); (D.W.B.)
- Correspondence: ; Tel.: +1-404-413-5503; Fax: +1-404-413-5505
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18
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Costas-Lago MC, Vila N, Rahman A, Besada P, Rozas I, Brea J, Loza MI, González-Romero E, Terán C. Novel Pyridazin-3(2 H)-one-Based Guanidine Derivatives as Potential DNA Minor Groove Binders with Anticancer Activity. ACS Med Chem Lett 2022; 13:463-469. [PMID: 35300077 PMCID: PMC8919506 DOI: 10.1021/acsmedchemlett.1c00633] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Novel aryl guanidinium analogues containing the pyridazin-3(2H)-one core were proposed as minor groove binders (MGBs) with the support of molecular docking studies. The target dicationic or monocationic compounds, which show the guanidium group at different positions of the pyridazinone moiety, were synthesized using the corresponding silyl-protected pyridazinones as key intermediates. Pyridazinone scaffolds were converted into the adequate bromoalkyl derivatives, which by reaction with N,N'-di-Boc-protected guanidine followed by acid hydrolysis provided the hydrochloride salts 1-14 in good yields. The ability of new pyridazin-3(2H)-one-based guanidines as DNA binders was studied by means of DNA UV-thermal denaturation experiments. Their antiproliferative activity was also explored in three cancer cell lines (NCI-H460, A2780, and MCF-7). Compounds 1-4 with a bis-guanidinium structure display a weak DNA binding affinity and exhibit a reasonable cellular viability inhibition percentage in the three cancer cell lines studied.
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Affiliation(s)
- María Carmen Costas-Lago
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Noemí Vila
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Adeyemi Rahman
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Pedro Besada
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - José Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, España
| | - María Isabel Loza
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, España
| | - Elisa González-Romero
- Departamento de Química Analítica y Alimentaria, Universidade de Vigo, 36310 Vigo, España
| | - Carmen Terán
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
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19
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Zhang S, Zhao S, Qi Y, Li B, Wang H, Pan Z, Xue H, Jin C, Qiu W, Chen Z, Guo Q, Fan Y, Xu J, Gao Z, Wang S, Guo X, Deng L, Ni S, Xue F, Wang J, Zhao R, Li G. SPI1-induced downregulation of FTO promotes GBM progression by regulating pri-miR-10a processing in an m6A-dependent manner. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:699-717. [PMID: 35317283 PMCID: PMC8905236 DOI: 10.1016/j.omtn.2021.12.035] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 12/29/2021] [Indexed: 12/15/2022]
Abstract
As one of the most common post-transcriptional modifications of mRNAs and noncoding RNAs, N6-methyladenosine (m6A) modification regulates almost every aspect of RNA metabolism. Evidence indicates that dysregulation of m6A modification and associated proteins contributes to glioblastoma (GBM) progression. However, the function of fat mass and obesity-associated protein (FTO), an m6A demethylase, has not been systematically and comprehensively explored in GBM. Here, we found that decreased FTO expression in clinical specimens correlated with higher glioma grades and poorer clinical outcomes. Functionally, FTO inhibited growth and invasion in GBM cells in vitro and in vivo. Mechanistically, FTO regulated the m6A modification of primary microRNA-10a (pri-miR-10a), which could be recognized by reader HNRNPA2B1, recruiting the microRNA microprocessor complex protein DGCR8 and mediating pri-miR-10a processing. Furthermore, the transcriptional activity of FTO was inhibited by the transcription factor SPI1, which could be specifically disrupted by the SPI1 inhibitor DB2313. Treatment with this inhibitor restored endogenous FTO expression and decreased GBM tumor burden, suggesting that FTO may serve as a novel prognostic indicator and therapeutic molecular target of GBM.
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Affiliation(s)
- Shouji Zhang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shulin Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Yanhua Qi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Ziwen Pan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Chuandi Jin
- Institute for Medical Dataology of Shandong University, Jinan, People’s Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong Province, People’s Republic of China
| | - Wei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Zihang Chen
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Qindong Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shaobo Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Lin Deng
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Shilei Ni
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
| | - Fuzhong Xue
- Institute for Medical Dataology of Shandong University, Jinan, People’s Republic of China
- Department of Epidemiology and Health Statistics, School of Public Health, Shandong University, Jinan, Shandong Province, People’s Republic of China
| | - Jian Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Department of Biomedicine, University of Bergen, Jonas Lies Vei 91, 5009 Bergen, Norway
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Corresponding author: Rongrong Zhao, Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China.
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan, Shandong 250012, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan, Shandong 250012, China
- Corresponding author: Gang Li, Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China.
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20
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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21
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Farahat AA, Iwamoto S, Roche M, Boykin DW. Facile synthesis of benzobisimidazole and bibenzimidazole‐based bisnitriles as potential precursors for
DNA
minor groove binders. J Heterocycl Chem 2021. [DOI: 10.1002/jhet.4353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Abdelbasset A. Farahat
- Master of Pharmaceutical Sciences Program California Northstate University Elk Grove California USA
- Faculty of Pharmacy Mansoura University Mansoura Egypt
| | - Satori Iwamoto
- Master of Pharmaceutical Sciences Program California Northstate University Elk Grove California USA
| | - Michael Roche
- Master of Pharmaceutical Sciences Program California Northstate University Elk Grove California USA
| | - David W. Boykin
- Chemistry Department Georgia State University Atlanta Georgia USA
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22
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Han R, Yuan T, Yang Z, Zhang Q, Wang WW, Lin LB, Zhu MQ, Gao JM. Ulmoidol, an unusual nortriterpenoid from Eucommia ulmoides Oliv. Leaves prevents neuroinflammation by targeting the PU.1 transcriptional signaling pathway. Bioorg Chem 2021; 116:105345. [PMID: 34560559 DOI: 10.1016/j.bioorg.2021.105345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 08/24/2021] [Accepted: 09/07/2021] [Indexed: 11/19/2022]
Abstract
Chronic neuroinflammation is closely associated with the development of neurodegenerative diseases, including Alzheimer's disease (AD). In the current study, 13 anti-neuroinflammatory compounds were isolated from Eucommia ulmoides Oliv. leaves. Among these compounds, trans-sinapaldehyde (6), 3',4',5,7-tetrahydroxy-3-methylflavone (7), and amarusine A (13) were isolated from E. ulmoides leaves for the first time. The ursane-type C29-triterpenoid, ulmoidol (ULM, 9), significantly inhibited the production of proinflammatory mediators and reduced the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2). Moreover, ULM inhibited the cluster of differentiation 14 (CD14)/Toll-like receptor 4 (TLR4) signaling pathway and consequently limited the activation of nuclear factor kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways. Notably, electrophoretic mobility shift assay (EMSA) and molecular docking analyses indicated that ULM could prevent PU box binding-1 (PU.1) from binding to DNA, suggesting that PU.1 might be a potential ULM target. In conclusion, ULM alleviates neuroinflammatory responses in microglia, which could be partly explained by its targeting of PU.1 and the resulting suppression of the TLR4/MAPK/NF-κB signaling pathways. These results suggested that ULM may have therapeutic potential as an agent for treating neuroinflammation-related neurodegenerative diseases.
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Affiliation(s)
- Rui Han
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Tian Yuan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Zhi Yang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Qiang Zhang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Wei-Wei Wang
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Li-Bin Lin
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China
| | - Ming-Qiang Zhu
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
| | - Jin-Ming Gao
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
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23
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Le Coz C, Nguyen DN, Su C, Nolan BE, Albrecht AV, Xhani S, Sun D, Demaree B, Pillarisetti P, Khanna C, Wright F, Chen PA, Yoon S, Stiegler AL, Maurer K, Garifallou JP, Rymaszewski A, Kroft SH, Olson TS, Seif AE, Wertheim G, Grant SFA, Vo LT, Puck JM, Sullivan KE, Routes JM, Zakharova V, Shcherbina A, Mukhina A, Rudy NL, Hurst ACE, Atkinson TP, Boggon TJ, Hakonarson H, Abate AR, Hajjar J, Nicholas SK, Lupski JR, Verbsky J, Chinn IK, Gonzalez MV, Wells AD, Marson A, Poon GMK, Romberg N. Constrained chromatin accessibility in PU.1-mutated agammaglobulinemia patients. J Exp Med 2021; 218:212070. [PMID: 33951726 PMCID: PMC8105723 DOI: 10.1084/jem.20201750] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/09/2021] [Accepted: 03/16/2021] [Indexed: 12/19/2022] Open
Abstract
The pioneer transcription factor (TF) PU.1 controls hematopoietic cell fate by decompacting stem cell heterochromatin and allowing nonpioneer TFs to enter otherwise inaccessible genomic sites. PU.1 deficiency fatally arrests lymphopoiesis and myelopoiesis in mice, but human congenital PU.1 disorders have not previously been described. We studied six unrelated agammaglobulinemic patients, each harboring a heterozygous mutation (four de novo, two unphased) of SPI1, the gene encoding PU.1. Affected patients lacked circulating B cells and possessed few conventional dendritic cells. Introducing disease-similar SPI1 mutations into human hematopoietic stem and progenitor cells impaired early in vitro B cell and myeloid cell differentiation. Patient SPI1 mutations encoded destabilized PU.1 proteins unable to nuclear localize or bind target DNA. In PU.1-haploinsufficient pro–B cell lines, euchromatin was less accessible to nonpioneer TFs critical for B cell development, and gene expression patterns associated with the pro– to pre–B cell transition were undermined. Our findings molecularly describe a novel form of agammaglobulinemia and underscore PU.1’s critical, dose-dependent role as a hematopoietic euchromatin gatekeeper.
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Affiliation(s)
- Carole Le Coz
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - David N Nguyen
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Chun Su
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Brian E Nolan
- Division of Rheumatology, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL.,Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, IL
| | - Amanda V Albrecht
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Suela Xhani
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Di Sun
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Benjamin Demaree
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA
| | - Piyush Pillarisetti
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Caroline Khanna
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Francis Wright
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA
| | - Peixin Amy Chen
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA
| | - Samuel Yoon
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy L Stiegler
- Departments of Pharmacology, Yale University, New Haven, CT
| | - Kelly Maurer
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA
| | - James P Garifallou
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Amy Rymaszewski
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Steven H Kroft
- Department of Pathology, Medical College of Wisconsin, Milwaukee, WI
| | - Timothy S Olson
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Alix E Seif
- Division of Oncology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Gerald Wertheim
- Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Struan F A Grant
- Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Division of Diabetes and Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Linda T Vo
- Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA
| | - Jennifer M Puck
- Division of Allergy, Immunology, and Bone Marrow Transplantation, Department of Pediatrics, University of California, San Francisco, CA.,University of California San Francsico Institute for Human Genetics and Smith Cardiovascular Research Institute, University of California, San Francisco, CA.,UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA
| | - Kathleen E Sullivan
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - John M Routes
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Viktoria Zakharova
- Laboratory of Molecular Biology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Mukhina
- Department of Immunology, Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natasha L Rudy
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL
| | - Anna C E Hurst
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL.,Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - T Prescott Atkinson
- Department of Pediatrics, University of Alabama at Birmingham, Birmingham, AL
| | - Titus J Boggon
- Departments of Pharmacology, Yale University, New Haven, CT.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA
| | - Adam R Abate
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA.,University of California Berkeley-University of California San Francisco Graduate Program in Bioengineering, University of California, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA
| | - Joud Hajjar
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Sarah K Nicholas
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - James R Lupski
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX.,Texas Children's Hospital, Houston, TX.,Baylor-Hopkins Center for Mendelian Genomics, Houston, TX
| | - James Verbsky
- Division of Allergy and Immunology, Department of Pediatrics, Medical College of Wisconsin, Milwaukee, WI
| | - Ivan K Chinn
- William T. Shearer Center for Human Immunobiology, Texas Children's Hospital, Houston, TX.,Department of Immunology, Allergy and Rheumatology, Baylor College of Medicine, Houston, TX
| | - Michael V Gonzalez
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA
| | - Andrew D Wells
- Center for Spatial and Functional Genomics, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Alex Marson
- Division of Infectious Diseases, Department of Medicine, University of California San Francisco, San Francisco, CA.,Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA.,Diabetes Center, University of California San Francisco, San Francisco, CA.,Innovative Genomics Institute, University of California Berkeley, Berkeley, CA.,Gladstone-University of California San Francisco Institute of Genomic Immunology, San Francisco, CA.,Chan Zuckerberg Biohub, San Francisco, CA.,Parker Institute for Cancer Immunotherapy, San Francisco, CA
| | - Gregory M K Poon
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA
| | - Neil Romberg
- Division of Immunology and Allergy, Children's Hospital of Philadelphia, Philadelphia, PA.,Department of Pediatrics, Perelman School of Medicine, Philadelphia, PA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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24
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Ha VLT, Erlitzki N, Farahat AA, Kumar A, Boykin DW, Poon GMK. Dissecting Dynamic and Hydration Contributions to Sequence-Dependent DNA Minor Groove Recognition. Biophys J 2020; 119:1402-1415. [PMID: 32898478 DOI: 10.1016/j.bpj.2020.08.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 07/13/2020] [Accepted: 08/10/2020] [Indexed: 10/23/2022] Open
Abstract
Sequence selectivity is a critical attribute of DNA-binding ligands and underlines the need for detailed molecular descriptions of binding in representative sequence contexts. We investigated the binding and volumetric properties of DB1976, a model bis(benzimidazole)-selenophene diamidine compound with emerging therapeutic potential in acute myeloid leukemia, debilitating fibroses, and obesity-related liver dysfunction. To sample the scope of cognate DB1976 target sites, we evaluated three dodecameric duplexes spanning >103-fold in binding affinity. The attendant changes in partial molar volumes varied substantially, but not in step with binding affinity, suggesting distinct modes of interactions in these complexes. Specifically, whereas optimal binding was associated with loss of hydration water, low-affinity binding released more hydration water. Explicit-atom molecular dynamics simulations showed that minor groove binding perturbed the conformational dynamics and hydration at the termini and interior of the DNA in a sequence-dependent manner. The impact of these distinct local dynamics on hydration was experimentally validated by domain-specific interrogation of hydration with salt, which probed the charged axial surfaces of oligomeric DNA preferentially over the uncharged termini. Minor groove recognition by DB1976, therefore, generates dynamically distinct domains that can make favorable contributions to hydration release in both high- and low-affinity binding. Because ligand binding at internal sites of DNA oligomers modulates dynamics at the termini, the results suggest both short- and long-range dynamic effects along the DNA target that can influence their effectiveness as low-MW competitors of protein binding.
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Affiliation(s)
- Van L T Ha
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Noa Erlitzki
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia; Department of Pharmaceutical and Medicinal Chemistry, California Northstate University, Elk Grove, California
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, Georgia; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, Georgia.
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25
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Wu Y, Zhu H, Wu H. PTEN in Regulating Hematopoiesis and Leukemogenesis. Cold Spring Harb Perspect Med 2020; 10:cshperspect.a036244. [PMID: 31712222 DOI: 10.1101/cshperspect.a036244] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
PTEN is one of the most frequently mutated tumor suppressor genes in human cancers. By counteracting the PI3K/AKT/mTOR pathway, PTEN plays an essential role in regulating hematopoietic stem cells (HSCs) self-renewal, migration, lineage commitment, and differentiation. PTEN also plays important roles in suppressing leukemogenesis, especially T-cell acute lymphoblastic leukemia (T-ALL). Herein, we will review the function of PTEN in regulating hematopoiesis and leukemogenesis and discuss potential therapeutic approaches against leukemia with PTEN mutations.
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Affiliation(s)
- Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Beijing Advanced Innovation Center for Genomics, Peking University, Beijing 100871, China
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26
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Liu Q, Yu J, Wang L, Tang Y, Zhou Q, Ji S, Wang Y, Santos L, Haeusler RA, Que J, Rajbhandari P, Lei X, Valenti L, Pajvani UB, Qin J, Qiang L. Inhibition of PU.1 ameliorates metabolic dysfunction and non-alcoholic steatohepatitis. J Hepatol 2020; 73:361-370. [PMID: 32135178 DOI: 10.1016/j.jhep.2020.02.025] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND & AIMS Obesity is a well-established risk factor for type 2 diabetes (T2D) and non-alcoholic steatohepatitis (NASH), but the underlying mechanisms remain incompletely understood. Herein, we aimed to identify novel pathogenic factors (and possible therapeutic targets) underlying metabolic dysfunction in the liver. METHODS We applied a tandem quantitative proteomics strategy to enrich and identify transcription factors (TFs) induced in the obese liver. We used flow cytometry of liver cells to analyze the source of the induced TFs. We employed conditional knockout mice, shRNA, and small-molecule inhibitors to test the metabolic consequences of the induction of identified TFs. Finally, we validated mouse data in patient liver biopsies. RESULTS We identified PU.1/SPI1, the master hematopoietic regulator, as one of the most upregulated TFs in livers from diet-induced obese (DIO) and genetically obese (db/db) mice. Targeting PU.1 in the whole liver, but not hepatocytes alone, significantly improved glucose homeostasis and suppressed liver inflammation. Consistently, treatment with the PU.1 inhibitor DB1976 markedly reduced inflammation and improved glucose homeostasis and dyslipidemia in DIO mice, and strongly suppressed glucose intolerance, liver steatosis, inflammation, and fibrosis in a dietary NASH mouse model. Furthermore, hepatic PU.1 expression was positively correlated with insulin resistance and inflammation in liver biopsies from patients. CONCLUSIONS These data suggest that the elevated hematopoietic factor PU.1 promotes liver metabolic dysfunction, and may be a useful therapeutic target for obesity, insulin resistance/T2D, and NASH. LAY SUMMARY Expression of the immune regulator PU.1 is increased in livers of obese mice and people. Blocking PU.1 improved glucose homeostasis, and reduced liver steatosis, inflammation and fibrosis in mouse models of non-alcoholic steatohepatitis. Inhibition of PU.1 is thus a potential therapeutic strategy for treating obesity-associated liver dysfunction and metabolic diseases.
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Affiliation(s)
- Qiongming Liu
- Naomi Berrie Diabetes Center, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, 10032, USA; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center at Beijing), Beijing 102206, China
| | - Junjie Yu
- Naomi Berrie Diabetes Center, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, USA
| | - Liheng Wang
- Naomi Berrie Diabetes Center, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, USA
| | - Yuliang Tang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Quan Zhou
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center at Beijing), Beijing 102206, China
| | - Shuhui Ji
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center at Beijing), Beijing 102206, China
| | - Yi Wang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Luis Santos
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Rebecca A Haeusler
- Naomi Berrie Diabetes Center, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, 10032, USA
| | - Jianwen Que
- Columbia Center for Human Development and Department of Medicine, Columbia University, New York, NY 10032
| | - Prashant Rajbhandari
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, United States
| | - Xiaoguang Lei
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi Milano, and Internal Medicine and Metabolic Diseases, Fondazione IRCCS Ca' Granda Ospedale Policlinico, Milan, Italy
| | - Utpal B Pajvani
- Naomi Berrie Diabetes Center, Department of Medicine, College of Physicians and Surgeons, Columbia University, New York, New York, 10032, USA.
| | - Jun Qin
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center at Beijing), Beijing 102206, China; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, 77030, USA.
| | - Li Qiang
- Naomi Berrie Diabetes Center, Department of Pathology and Cell Biology, College of Physicians and Surgeons, Columbia University, New York, 10032, USA.
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27
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Martin-Estebane M, Gomez-Nicola D. Targeting Microglial Population Dynamics in Alzheimer's Disease: Are We Ready for a Potential Impact on Immune Function? Front Cell Neurosci 2020; 14:149. [PMID: 32581720 PMCID: PMC7289918 DOI: 10.3389/fncel.2020.00149] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 05/05/2020] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia, affecting two-thirds of people with dementia in the world. To date, no disease-modifying treatments are available to stop or delay the progression of AD. This chronic neurodegenerative disease is dominated by a strong innate immune response, whereby microglia plays a central role as the main resident macrophage of the brain. Recent genome-wide association studies (GWASs) have identified single-nucleotide polymorphisms (SNPs) located in microglial genes and associated with a delayed onset of AD, highlighting the important role of these cells on the onset and/or progression of the disease. These findings have increased the interest in targeting microglia-associated neuroinflammation as a potentially disease-modifying therapeutic approach for AD. In this review we provide an overview on the contribution of microglia to the pathophysiology of AD, focusing on the main regulatory pathways controlling microglial population dynamics during the neuroinflammatory response, such as the colony-stimulating factor 1 receptor (CSF1R), its ligands (the colony-stimulating factor 1 and interleukin 34) and the transcription factor PU.1. We also discuss the current therapeutic strategies targeting proliferation to modulate microglia-associated neuroinflammation and their potential impact on peripheral immune cell populations in the short and long-term. Understanding the effects of immunomodulatory approaches on microglia and other immune cell types might be critical for developing specific, effective, and safe therapies for neurodegenerative diseases.
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Affiliation(s)
- Maria Martin-Estebane
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton, United Kingdom
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28
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Guo P, Farahat AA, Paul A, Kumar A, Boykin DW, Wilson WD. Extending the σ-Hole Motif for Sequence-Specific Recognition of the DNA Minor Groove. Biochemistry 2020; 59:1756-1768. [PMID: 32293884 DOI: 10.1021/acs.biochem.0c00090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The majority of current drugs against diseases, such as cancer, can bind to one or more sites in a protein and inhibit its activity. There are, however, well-known limits on the number of druggable proteins, and complementary current drugs with compounds that could selectively target DNA or RNA would greatly enhance the availability of cellular probes and therapeutic progress. We are focusing on the design of sequence-specific DNA minor groove binders that, for example, target the promoter sites of transcription factors involved in a disease. We have started with AT-specific minor groove binders that are known to enter human cells and have entered clinical trials. To broaden the sequence-specific recognition of these compounds, several modules that have H-bond acceptors that strongly and specifically recognize G·C base pairs were identified. A lead module is a thiophene-N-alkyl-benzimidazole σ-hole-based system with terminal phenyl-amidines that have excellent affinity and selectivity for a G·C base pair in the minor groove. Efforts are now focused on optimizing this module. In this work, we are evaluating modifications to the compound aromatic system with the goal of improving GC selectivity and affinity. The lead compounds retain the thiophene-N-alkyl-BI module but have halogen substituents adjacent to an amidine group on the terminal phenyl-amidine. The optimum compounds must have strong affinity and specificity with a residence time of at least 100 s.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States.,Master of Pharmaceutical Sciences Program, California Northstate University, 9700 West Taron Drive, Elk Grove, California 95757, United States
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, 50 Decatur Street Southeast, Atlanta, Georgia 30303, United States
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29
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Farahat AA, Guo P, Shoeib H, Paul A, Boykin DW, Wilson WD. Small Sequence-Sensitive Compounds for Specific Recognition of the G⋅C Base Pair in DNA Minor Groove. Chemistry 2020; 26:4539-4551. [PMID: 31884714 PMCID: PMC7265973 DOI: 10.1002/chem.201904396] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/10/2019] [Indexed: 12/24/2022]
Abstract
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3 )3 ]2 ) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.
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Affiliation(s)
- Abdelbasset A. Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Hadir Shoeib
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - David W. Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
| | - W. David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St SE, Atlanta, GA 30303, USA
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Liu B, Bashkin JK, Poon GMK, Wang S, Wang S, Wilson WD. Modulating DNA by polyamides to regulate transcription factor PU.1-DNA binding interactions. Biochimie 2019; 167:1-11. [PMID: 31445072 DOI: 10.1016/j.biochi.2019.08.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022]
Abstract
Hairpin polyamides are synthetic small molecules that bind DNA minor groove sequence-selectively and, in many sequences, induce widening of the minor groove and compression of the major groove. The structural distortion of DNA caused by polyamides has enhanced our understanding of the regulation of DNA-binding proteins via polyamides. Polyamides have DNA binding affinities that are comparable to those proteins, therefore, can potentially be used as therapeutic agents to treat diseases caused by aberrant gene expression. In fact, many diseases are characterized by over- or under-expressed genes. PU.1 is a transcription factor that regulates many immune system genes. Aberrant expression of PU.1 has been associated with the development of acute myeloid leukemia (AML). We have, therefore, designed and synthesized ten hairpin polyamides to investigate their capacity in controlling the PU.1-DNA interaction. Our results showed that nine of the polyamides disrupt PU.1-DNA binding and the inhibition capacity strongly correlates with binding affinity. One molecule, FH1024, was observed forming a FH1024-PU.1-DNA ternary complex instead of inhibiting PU.1-DNA binding. This is the first report of a small molecule that is potentially a weak agonist that recruits PU.1 to DNA. This finding sheds light on the design of polyamides that exhibit novel regulatory mechanisms on protein-DNA binding.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - James K Bashkin
- Department of Chemistry & Biochemistry, Center for Nanoscience, University of Missouri-St. Louis, St. Louis, MO, 63121, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - Siming Wang
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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31
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Luongo F, Colonna F, Calapà F, Vitale S, Fiori ME, De Maria R. PTEN Tumor-Suppressor: The Dam of Stemness in Cancer. Cancers (Basel) 2019; 11:E1076. [PMID: 31366089 PMCID: PMC6721423 DOI: 10.3390/cancers11081076] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 07/24/2019] [Accepted: 07/26/2019] [Indexed: 12/11/2022] Open
Abstract
PTEN is one of the most frequently inactivated tumor suppressor genes in cancer. Loss or variation in PTEN gene/protein levels is commonly observed in a broad spectrum of human cancers, while germline PTEN mutations cause inherited syndromes that lead to increased risk of tumors. PTEN restrains tumorigenesis through different mechanisms ranging from phosphatase-dependent and independent activities, subcellular localization and protein interaction, modulating a broad array of cellular functions including growth, proliferation, survival, DNA repair, and cell motility. The main target of PTEN phosphatase activity is one of the most significant cell growth and pro-survival signaling pathway in cancer: PI3K/AKT/mTOR. Several shreds of evidence shed light on the critical role of PTEN in normal and cancer stem cells (CSCs) homeostasis, with its loss fostering the CSC compartment in both solid and hematologic malignancies. CSCs are responsible for tumor propagation, metastatic spread, resistance to therapy, and relapse. Thus, understanding how alterations of PTEN levels affect CSC hallmarks could be crucial for the development of successful therapeutic approaches. Here, we discuss the most significant findings on PTEN-mediated control of CSC state. We aim to unravel the role of PTEN in the regulation of key mechanisms specific for CSCs, such as self-renewal, quiescence/cell cycle, Epithelial-to-Mesenchymal-Transition (EMT), with a particular focus on PTEN-based therapy resistance mechanisms and their exploitation for novel therapeutic approaches in cancer treatment.
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Affiliation(s)
- Francesca Luongo
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Francesca Colonna
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Federica Calapà
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Sara Vitale
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
| | - Micol E Fiori
- Department of Oncology and Molecular Medicine, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Ruggero De Maria
- Istituto di Patologia Generale, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy.
- Scientific Vice-Direction, Fondazione Policlinico Universitario "A. Gemelli"-I.R.C.C.S., Largo Francesco Vito 1-8, 00168 Rome, Italy.
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32
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Albrecht AV, Kim HM, Poon GMK. Mapping interfacial hydration in ETS-family transcription factor complexes with DNA: a chimeric approach. Nucleic Acids Res 2019; 46:10577-10588. [PMID: 30295801 PMCID: PMC6237740 DOI: 10.1093/nar/gky894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/21/2018] [Indexed: 11/12/2022] Open
Abstract
Hydration of interfaces is a major determinant of target specificity in protein/DNA interactions. Interfacial hydration is a highly variable feature in DNA recognition by ETS transcription factors and functionally relates to cellular responses to osmotic stress. To understand how hydration is mediated in the conserved ETS/DNA binding interface, secondary structures comprising the DNA contact surface of the strongly hydrated ETS member PU.1 were substituted, one at a time, with corresponding elements from its sparsely hydrated relative Ets-1. The resultant PU.1/Ets-1 chimeras exhibited variably reduced sensitivity to osmotic pressure, indicative of a distributed pattern of interfacial hydration in wildt-ype PU.1. With the exception of the recognition helix H3, the chimeras retained substantially high affinities. Ets-1 residues could therefore offset the loss of favorable hydration contributions in PU.1 via low-water interactions, but at the cost of decreased selectivity at base positions flanking the 5'-GGA-3' core consensus. Substitutions within H3 alone, which contacts the core consensus, impaired binding affinity and PU.1 transactivation in accordance with the evolutionary separation of the chimeric residues involved. The combined biophysical, bioinformatics and functional data therefore supports hydration as an evolved specificity determinant that endows PU.1 with more stringent sequence selection over its ancestral relative Ets-1.
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Affiliation(s)
- Amanda V Albrecht
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.,Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
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Gupta S, Tiwari N, Munde M. A Comprehensive Biophysical Analysis of the Effect of DNA Binding Drugs on Protamine-induced DNA Condensation. Sci Rep 2019; 9:5891. [PMID: 30971720 PMCID: PMC6458161 DOI: 10.1038/s41598-019-41975-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/13/2019] [Indexed: 11/21/2022] Open
Abstract
DNA condensation is a ubiquitous phenomenon in biology, yet the physical basis for it has remained elusive. Here, we have explored the mechanism of DNA condensation through the protamine-DNA interaction, and by examining on it the influence of DNA binding drugs. We observed that the DNA condensation is accompanied by B to Ψ-DNA transition as a result of DNA base pair distortions due to protamine binding, bringing about the formation of toroidal structure through coil-globule transition. The binding energetics suggested that electrostatic energy, bending energy and hydration energy must play crucial roles in DNA condensation. EtBr intercalation interferes with the protamine-DNA interaction, challenging the distortion of the DNA helix and separation of DNA base pairs by protamine. Thus, EtBr, by competing directly with protamine, resists the phenomenon of DNA condensation. On the contrary, netropsin impedes the DNA condensation by an allosteric mechanism, by resisting the probable DNA major groove bending by protamine. In summary, we demonstrate that drugs with distinct binding modes use different mechanism to interfere with DNA condensation.
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Affiliation(s)
- Sakshi Gupta
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Neha Tiwari
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Manoj Munde
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India.
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Depauw S, Lambert M, Jambon S, Paul A, Peixoto P, Nhili R, Morongiu L, Figeac M, Dassi C, Paul-Constant C, Billoré B, Kumar A, Farahat AA, Ismail MA, Mineva E, Sweat DP, Stephens CE, Boykin DW, Wilson WD, David-Cordonnier MH. Heterocyclic Diamidine DNA Ligands as HOXA9 Transcription Factor Inhibitors: Design, Molecular Evaluation, and Cellular Consequences in a HOXA9-Dependant Leukemia Cell Model. J Med Chem 2019; 62:1306-1329. [PMID: 30645099 PMCID: PMC6561105 DOI: 10.1021/acs.jmedchem.8b01448] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most transcription factors were for a long time considered as undruggable targets because of the absence of binding pockets for direct targeting. HOXA9, implicated in acute myeloid leukemia, is one of them. To date, only indirect targeting of HOXA9 expression or multitarget HOX/PBX protein/protein interaction inhibitors has been developed. As an attractive alternative by inhibiting the DNA binding, we selected a series of heterocyclic diamidines as efficient competitors for the HOXA9/DNA interaction through binding as minor groove DNA ligands on the HOXA9 cognate sequence. Selected DB818 and DB1055 compounds altered HOXA9-mediated transcription in luciferase assays, cell survival, and cell cycle, but increased cell death and granulocyte/monocyte differentiation, two main HOXA9 functions also highlighted using transcriptomic analysis of DB818-treated murine Hoxa9-transformed hematopoietic cells. Altogether, these data demonstrate for the first time the propensity of sequence-selective DNA ligands to inhibit HOXA9/DNA binding both in vitro and in a murine Hoxa9-dependent leukemic cell model.
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Affiliation(s)
- Sabine Depauw
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Mélanie Lambert
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Samy Jambon
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Paul Peixoto
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Raja Nhili
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Laura Morongiu
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Martin Figeac
- Functional and Structural Genomic Platform, Lille University, F-59000 Lille, France
| | - Christelle Dassi
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Charles Paul-Constant
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Benjamin Billoré
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Abdelbasset A. Farahat
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Mohamed A. Ismail
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
- Department of Chemistry, Faculty of Science, Mansoura University, Mansoura 35516, Egypt
| | - Ekaterina Mineva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Daniel P. Sweat
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30904, United States
| | - Chad E. Stephens
- Department of Chemistry and Physics, Augusta University, Augusta, GA 30904, United States
| | - David W. Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, United States
| | - Marie-Hélène David-Cordonnier
- UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), INSERM, University of Lille, Centre Hospitalier Universitaire de Lille, Institut pour la recherché sur le Cancer de Lille (IRCL), F-59045 Lille, France
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35
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Wohlfahrt T, Rauber S, Uebe S, Luber M, Soare A, Ekici A, Weber S, Matei AE, Chen CW, Maier C, Karouzakis E, Kiener HP, Pachera E, Dees C, Beyer C, Daniel C, Gelse K, Kremer AE, Naschberger E, Stürzl M, Butter F, Sticherling M, Finotto S, Kreuter A, Kaplan MH, Jüngel A, Gay S, Nutt SL, Boykin DW, Poon GMK, Distler O, Schett G, Distler JHW, Ramming A. PU.1 controls fibroblast polarization and tissue fibrosis. Nature 2019; 566:344-349. [PMID: 30700907 PMCID: PMC6526281 DOI: 10.1038/s41586-019-0896-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/21/2018] [Indexed: 02/06/2023]
Abstract
Fibroblasts are polymorphic cells with pleiotropic roles in organ morphogenesis, tissue homeostasis and immune responses. In fibrotic diseases, fibroblasts synthesize abundant amounts of extracellular matrix which lead to scaring and organ failure. In contrast, the hallmark feature of fibroblasts in arthritis is matrix degradation by the release of metalloproteinases and degrading enzymes, and subsequent tissue destruction. The mechanisms driving these functionally opposing pro-fibrotic and pro-inflammatory phenotypes of fibroblasts are enigmatic. We identified the transcription factor PU.1 as an essential orchestrator of the pro-fibrotic gene expression program. The interplay between transcriptional and post-transcriptional mechanisms which normally control PU.1 expression is perturbed in various fibrotic diseases, resulting in upregulation of PU.1, induction of fibrosis-associated gene sets, and a phenotypic switch in matrix-producing pro-fibrotic fibroblasts. In contrast, pharmacological and genetic inactivation of PU.1 disrupts the fibrotic network and enables re-programming of fibrotic fibroblasts into resting fibroblasts with regression of fibrosis in different organs.
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Affiliation(s)
- Thomas Wohlfahrt
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Simon Rauber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Steffen Uebe
- Institute of Human Genetics, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Markus Luber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alina Soare
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Arif Ekici
- Institute of Human Genetics, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Stefanie Weber
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alexandru-Emil Matei
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Chih-Wei Chen
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christiane Maier
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | | | - Hans P Kiener
- Division of Rheumatology, Department of Medicine III, Medical University of Vienna, Vienna, Austria
| | - Elena Pachera
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Clara Dees
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christian Beyer
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Christoph Daniel
- Department of Nephropathology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Kolja Gelse
- Department of Trauma Surgery, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas E Kremer
- Department of Internal Medicine 1, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Elisabeth Naschberger
- Division of Molecular and Experimental Surgery, Department of Surgery, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Michael Stürzl
- Division of Molecular and Experimental Surgery, Department of Surgery, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Falk Butter
- Quantitative Proteomics Group, Institute of Molecular Biology, Mainz, Germany
| | - Michael Sticherling
- Department of Dermatology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Susetta Finotto
- Department of Molecular Pneumology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Alexander Kreuter
- Department of Dermatology, Venereology and Allergology, HELIOS St. Elisabeth Klinik Oberhausen, University Witten-Herdecke, Oberhausen, Germany
| | - Mark H Kaplan
- Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Astrid Jüngel
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Steffen Gay
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Stephen L Nutt
- The Walter and Eliza Hall Institute of Medical Research, Molecular Immunology Division, Parkville, Victoria, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria, Australia
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA, USA
| | - Oliver Distler
- Department of Rheumatology, University Hospital Zurich, Zurich, Switzerland
| | - Georg Schett
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Jörg H W Distler
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany
| | - Andreas Ramming
- Department of Internal Medicine 3 - Rheumatology and Immunology, Friedrich-Alexander-University (FAU) Erlangen-Nürnberg and Universitätsklinikum Erlangen, Erlangen, Germany.
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Xia W, Luo P, Hua P, Ding P, Li C, Xu J, Zhou H, Gu Q. Discovery of a New Pterocarpan-Type Antineuroinflammatory Compound from Sophora tonkinensis through Suppression of the TLR4/NFκB/MAPK Signaling Pathway with PU.1 as a Potential Target. ACS Chem Neurosci 2019; 10:295-303. [PMID: 30223643 DOI: 10.1021/acschemneuro.8b00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Neuroinflammation underlies many neuro-degenerative diseases. In this paper, we report the identification of a new pterocarpan-type anti-inflammatory compound named sophotokin isolated from Sophora tonkinensis. S. tonkinensis has been used traditionally for treatment of conditions related to inflammation. Our initial screening showed that sophotokin dose-dependently inhibits lipopolysaccharide (LPS)-stimulated production of NO, TNF-α, PGE2, and IL-1β in microglial cells. This antineuroinflammatory effect was associated with sophotokin's blockade of LPS-induced production of the inflammatory mediators iNOS and COX-2. Western blot and qPCR analysis demonstrated that sophotokin inhibits both the p38-MAPK and NF-κB signal pathways. Further studies revealed that sophotokin also suppresses the expression of cluster differentiation 14 (CD14) in the toll-like receptor 4 (TLR4) signaling pathway. Following down-regulation of MyD88 and TRAF6, sophotokin inhibits the activation of the NF-κB and MAPK signal pathways in LPS-induced BV-2 cells. In silico studies suggested that sophotokin could interact with PU.1-DNA complex through hydrogen binding at sites 1 and 2 of the complex, blocking the DNA binding. This suggests that PU.1 may be a potential target of sophotokin. Taken together, these results suggest that sophotokin may have therapeutic potential for diseases related to neuroinflammation. The mechanism of antineuroinflammatory effects involves inhibition of the TLR4 signal pathway at the sites of NF-κB and MAPK with PU.1 as a likely upstream target.
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Affiliation(s)
- Wenjuan Xia
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Pan Luo
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Pei Hua
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Peng Ding
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Chanjuan Li
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Jun Xu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Huihao Zhou
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
| | - Qiong Gu
- Research Center for Drug Discovery, School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , People's Republic of China
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37
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Rahman A, O'Sullivan P, Rozas I. Recent developments in compounds acting in the DNA minor groove. MEDCHEMCOMM 2018; 10:26-40. [PMID: 30774852 DOI: 10.1039/c8md00425k] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/11/2018] [Indexed: 12/12/2022]
Abstract
The macromolecule that carries genetic information, DNA, is considered as an exceptional target for diseases depending on cellular division of malignant cells (i.e. cancer), microbes (i.e. bacteria) or parasites (i.e. protozoa). To aim for a comprehensive review to cover all aspects related to DNA targeting would be an impossible task and, hence, the objective of the present review is to present, from a medicinal chemistry point of view, recent developments of compounds targeting the minor groove of DNA. Accordingly, we discuss the medicinal chemistry aspects of heterocyclic small-molecules binding the DNA minor groove, as novel anticancer, antibacterial and antiparasitic agents.
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Affiliation(s)
- Adeyemi Rahman
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Patrick O'Sullivan
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
| | - Isabel Rozas
- School of Chemistry , Trinity Biomedical Sciences Institute , Trinity College Dublin , 152-160-Pearse Street , Dublin 2 , Ireland .
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38
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DNA recognition by linear indole-biphenyl DNA minor groove ligands. Biophys Chem 2018; 245:6-16. [PMID: 30513446 DOI: 10.1016/j.bpc.2018.11.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/15/2018] [Accepted: 11/22/2018] [Indexed: 11/21/2022]
Abstract
Linear heterocyclic cations are interesting DNA minor groove ligands due to their lack of isohelical curvature classically associated with groove-binding compounds. We determined the DNA binding properties of four related dications harboring a linear indole-biphenyl core: the diamidine DB1883, a ditetrahydropyrimidine derivative (DB1804), and their monocationic counterparts (DB1944 and DB2627). These compounds exhibit heterogeneity in binding in accordance with their structures. Whereas the monocations exhibit salt-sensitive 1:1 binding to the duplex 5'-CGCGAATTCGCG-3' (A2T2), the dications show a marked preference for a salt-insensitive 2:1 complex. The two binding modes are differentially modulated by salt and specific non-ionic co-solutes. For both dications, 2-methyl-2,4-pentanediol enforces 1:1 binding as observed crystallographically. Fluorescence quenching studies show self-association without DNA in a relative order that is correlated with preference for the 2:1 complex. The data support a structure-binding relationship in which favorable cation-π interactions drive dimer formation via antiparallel stacking of the linear indole-biphenyl cation motif.
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39
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Zhu H, Zhang L, Wu Y, Dong B, Guo W, Wang M, Yang L, Fan X, Tang Y, Liu N, Lei X, Wu H. T-ALL leukemia stem cell 'stemness' is epigenetically controlled by the master regulator SPI1. eLife 2018; 7:38314. [PMID: 30412053 PMCID: PMC6251627 DOI: 10.7554/elife.38314] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 11/09/2018] [Indexed: 12/17/2022] Open
Abstract
Leukemia stem cells (LSCs) are regarded as the origins and key therapeutic targets of leukemia, but limited knowledge is available on the key determinants of LSC 'stemness'. Using single-cell RNA-seq analysis, we identify a master regulator, SPI1, the LSC-specific expression of which determines the molecular signature and activity of LSCs in the murine Pten-null T-ALL model. Although initiated by PTEN-controlled β-catenin activation, Spi1 expression and LSC 'stemness' are maintained by a β-catenin-SPI1-HAVCR2 regulatory circuit independent of the leukemogenic driver mutation. Perturbing any component of this circuit either genetically or pharmacologically can prevent LSC formation or eliminate existing LSCs. LSCs lose their 'stemness' when Spi1 expression is silenced by DNA methylation, but Spi1 expression can be reactivated by 5-AZ treatment. Importantly, similar regulatory mechanisms may be also present in human T-ALL.
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Affiliation(s)
- Haichuan Zhu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Liuzhen Zhang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yilin Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Bingjie Dong
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Weilong Guo
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Mei Wang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Lu Yang
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Xiaoying Fan
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
| | - Yuliang Tang
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Ningshu Liu
- Drug Discovery Oncology, Bayer Pharmaceuticals, Berlin, Germany
| | - Xiaoguang Lei
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Hong Wu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Beijing Advanced Innovation Center for Genomics, Peking University, Beijing, China
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40
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Guo P, Farahat AA, Paul A, Harika NK, Boykin DW, Wilson WD. Compound Shape Effects in Minor Groove Binding Affinity and Specificity for Mixed Sequence DNA. J Am Chem Soc 2018; 140:14761-14769. [PMID: 30353731 PMCID: PMC6399738 DOI: 10.1021/jacs.8b08152] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
AT specific heterocyclic cations that bind in the DNA duplex minor groove have had major successes as cell and nuclear stains and as therapeutic agents which can effectively enter human cells. Expanding the DNA sequence recognition capability of the minor groove compounds could also expand their therapeutic targets and have an impact in many areas, such as modulation of transcription factor biological activity. Success in the design of mixed sequence binding compounds has been achieved with N-methylbenzimidazole ( N-MeBI) thiophenes which are preorganized to fit the shape of the DNA minor groove and H-bond to the -NH of G·C base pairs that project into the minor groove. Initial compounds bind strongly to a single G·C base pair in an AT context with a specificity ratio of 50 ( KD AT-GC/ KD AT) or less and this is somewhat low for biological use. We felt that modifications of compound shape could be used to probe local DNA microstructure in target mixed base pair sequences of DNA and potentially improve the compound binding selectivity. Modifications were made by increasing the size of the benzimidazole N-substituent, for example, by using N-isobutyl instead of N-Me, and by changing the molecular twist by introducing substitutions at specific positions on the aromatic core of the compounds. In both cases, we have been able to achieve a dramatic increase in binding specificity, including no detectible binding to pure AT sequences, without a significant loss in affinity to mixed base pair target sequences.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy , Mansoura University , Mansoura 35516 , Egypt
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics , Georgia State University , 50 Decatur Street South East , Atlanta , Georgia 30303 , United States
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41
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Pulugulla SH, Workman R, Rutter NW, Yang Z, Adamik J, Lupish B, Macar DA, El Abdouni S, Esposito EX, Galson DL, Camacho CJ, Madura JD, Auron PE. A combined computational and experimental approach reveals the structure of a C/EBPβ-Spi1 interaction required for IL1B gene transcription. J Biol Chem 2018; 293:19942-19956. [PMID: 30355733 DOI: 10.1074/jbc.ra118.005627] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Revised: 10/09/2018] [Indexed: 01/19/2023] Open
Abstract
We previously reported that transcription of the human IL1B gene, encoding the proinflammatory cytokine interleukin 1β, depends on long-distance chromatin looping that is stabilized by a mutual interaction between the DNA-binding domains (DBDs) of two transcription factors: Spi1 proto-oncogene at the promoter and CCAAT enhancer-binding protein (C/EBPβ) at a far-upstream enhancer. We have also reported that the C-terminal tail sequence beyond the C/EBPβ leucine zipper is critical for its association with Spi1 via an exposed residue (Arg-232) located within a pocket at one end of the Spi1 DNA-recognition helix. Here, combining in vitro interaction studies with computational docking and molecular dynamics of existing X-ray structures for the Spi1 and C/EBPβ DBDs, along with the C/EBPβ C-terminal tail sequence, we found that the tail sequence is intimately associated with Arg-232 of Spi1. The Arg-232 pocket was computationally screened for small-molecule binding aimed at IL1B transcription inhibition, yielding l-arginine, a known anti-inflammatory amino acid, revealing a potential for disrupting the C/EBPβ-Spi1 interaction. As evaluated by ChIP, cultured lipopolysaccharide (LPS)-activated THP-1 cells incubated with l-arginine had significantly decreased IL1B transcription and reduced C/EBPβ's association with Spi1 on the IL1B promoter. No significant change was observed in direct binding of either Spi1 or C/EBPβ to cognate DNA and in transcription of the C/EBPβ-dependent IL6 gene in the same cells. These results support the notion that disordered sequences extending from a leucine zipper can mediate protein-protein interactions and can serve as druggable targets for regulating gene promoter activity.
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Affiliation(s)
- Sree H Pulugulla
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Riley Workman
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Nathan W Rutter
- Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Zhiyong Yang
- the Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02115
| | - Juraj Adamik
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213
| | - Brian Lupish
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - David A Macar
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Samir El Abdouni
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | | | - Deborah L Galson
- the Department of Medicine, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213,; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219
| | - Carlos J Camacho
- the Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260
| | - Jeffry D Madura
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; Chemistry and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282
| | - Philip E Auron
- From the Departments of Biological Sciences and Biochemistry, Duquesne University, Pittsburgh, Pennsylvania 15282; the Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania 15219.
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42
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Jenquin JR, Coonrod LA, Silverglate QA, Pellitier NA, Hale MA, Xia G, Nakamori M, Berglund JA. Furamidine Rescues Myotonic Dystrophy Type I Associated Mis-Splicing through Multiple Mechanisms. ACS Chem Biol 2018; 13:2708-2718. [PMID: 30118588 DOI: 10.1021/acschembio.8b00646] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an autosomal dominant, CTG•CAG microsatellite expansion disease. Expanded CUG repeat RNA sequester the muscleblind-like (MBNL) family of RNA-binding proteins, thereby disrupting their normal cellular function which leads to global mis-regulation of RNA processing. Previously, the small molecule furamidine was shown to reduce CUG foci and rescue mis-splicing in a DM1 HeLa cell model and to rescue mis-splicing in the HSALR DM1 mouse model, but furamidine's mechanism of action was not explored. Here we use a combination of biochemical, cell toxicity, and genomic studies in DM1 patient-derived myotubes and the HSALR DM1 mouse model to investigate furamidine's mechanism of action. Mis-splicing rescue was observed in DM1 myotubes and the HSALR DM1 mouse with furamidine treatment. Interestingly, while furamidine was found to bind CTG•CAG repeat DNA with nanomolar affinity, a reduction in expanded CUG repeat transcript levels was observed in the HSALR DM1 mouse but not DM1 patient-derived myotubes. Further investigation in these cells revealed that furamidine treatment at nanomolar concentrations led to up-regulation of MBNL1 and MBNL2 protein levels and a reduction of ribonuclear foci. Additionally, furamidine was shown to bind CUG RNA with nanomolar affinity and disrupted the MBNL1 -CUG RNA complex in vitro at micromolar concentrations. Furamidine's likely promiscuous interactions in vitro and in vivo appear to affect multiple pathways in the DM1 mechanism to rescue mis-splicing, yet surprisingly furamidine was shown globally to rescue many mis-splicing events with only modest off-target effects on gene expression in the HSALR DM1 mouse model. Importantly, over 20% of the differentially expressed genes were shown to be returned, to varying degrees, to wild-type expression levels.
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Affiliation(s)
- Jana R. Jenquin
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Leslie A. Coonrod
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Quinn A. Silverglate
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Natalie A. Pellitier
- Department of Biology, University of Oregon, Eugene, Oregon 97403, United States
| | - Melissa A. Hale
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - Guangbin Xia
- Department of Neurology and Neuroscience, University of New Mexico School of Medicine, Albuquerque, New Mexico 87131, United States
| | - Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka 565-0871, Japan
| | - J. Andrew Berglund
- Department of Biochemistry & Molecular Biology, Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
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43
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Lambert M, Jambon S, Depauw S, David-Cordonnier MH. Targeting Transcription Factors for Cancer Treatment. Molecules 2018; 23:molecules23061479. [PMID: 29921764 PMCID: PMC6100431 DOI: 10.3390/molecules23061479] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 06/11/2018] [Accepted: 06/15/2018] [Indexed: 12/15/2022] Open
Abstract
Transcription factors are involved in a large number of human diseases such as cancers for which they account for about 20% of all oncogenes identified so far. For long time, with the exception of ligand-inducible nuclear receptors, transcription factors were considered as “undruggable” targets. Advances knowledge of these transcription factors, in terms of structure, function (expression, degradation, interaction with co-factors and other proteins) and the dynamics of their mode of binding to DNA has changed this postulate and paved the way for new therapies targeted against transcription factors. Here, we discuss various ways to target transcription factors in cancer models: by modulating their expression or degradation, by blocking protein/protein interactions, by targeting the transcription factor itself to prevent its DNA binding either through a binding pocket or at the DNA-interacting site, some of these inhibitors being currently used or evaluated for cancer treatment. Such different targeting of transcription factors by small molecules is facilitated by modern chemistry developing a wide variety of original molecules designed to specifically abort transcription factor and by an increased knowledge of their pathological implication through the use of new technologies in order to make it possible to improve therapeutic control of transcription factor oncogenic functions.
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Affiliation(s)
- Mélanie Lambert
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Samy Jambon
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Sabine Depauw
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
| | - Marie-Hélène David-Cordonnier
- INSERM UMR-S1172-JPARC (Jean-Pierre Aubert Research Center), Lille University and Hospital Center (CHU-Lille), Institut pour la Recherche sur le Cancer de Lille (IRCL), Place de Verdun, F-59045 Lille, France.
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44
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Patent highlights from December 2017 to January 2018. Pharm Pat Anal 2018; 7:111-119. [PMID: 29676211 DOI: 10.4155/ppa-2018-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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45
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Paul A, Kumar A, Nanjunda R, Farahat AA, Boykin DW, Wilson WD. Systematic synthetic and biophysical development of mixed sequence DNA binding agents. Org Biomol Chem 2018; 15:827-835. [PMID: 27995240 DOI: 10.1039/c6ob02390h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
It is now well established that, although only about 5% of the human genome codes for protein, most of the DNA has some function, such as synthesis of specific, functional RNAs and/or control of gene expression. These functional sequences open immense possibilities in both biotechnology and therapeutics for the use of cell-permeable, small molecules that can bind mixed-base pair sequences of DNA for regulation of genomic functions. Unfortunately very few types of modules have been designed to recognize mixed DNA sequences and for progress in targeting specific genes, it is essential to have additional classes of compounds. Compounds that can be rationally designed from established modules and which can bind strongly to mixed base pair DNA sequences are especially attractive. Based on extensive experience in design of minor-groove agents for AT recognition, a small library of compounds with two AT specific binding modules, connected through linkers which can recognize the G·C base pairs, were prepared. The compound-DNA interactions were evaluated with a powerful array of biophysical methods and the results show that some pyridyl-linked compounds bind with the target sequence with sub-nanomolar KD, with very slow dissociation kinetics and 200 times selectivity over the related sequence without a G·C base pair. Interestingly, a set of compounds with AT module connected by different linkers shows cooperative dimer recognition of related sequences. This type of design approach can be expanded to additional modules for recognition of a wide variety of sequences.
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Affiliation(s)
- Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - Rupesh Nanjunda
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Janssen Research and Development, 1400 McKean Rd, Spring House, PA 19477, USA
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA. and Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303-3083, USA.
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Liu B, Wang S, Aston K, Koeller KJ, Kermani SFH, Castañeda CH, Scuderi MJ, Luo R, Bashkin JK, Wilson WD. β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding. Org Biomol Chem 2018; 15:9880-9888. [PMID: 29143012 DOI: 10.1039/c7ob02513k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA-DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif. The λB motif is also a strong binding promoter site of the major groove targeting transcription factor PU.1. The PA binding affinities and kinetics were evaluated using a spectrum of powerful biophysical methods: thermal melting, biosensor surface plasmon resonance and circular dichroism. The results show that β inserts affect PA-DNA interactions in a number and position dependent manner. Specifically, a β replacement between two imidazole heterocycles (ImβIm) generally strengthens binding. In addition, N-terminal cationic groups can accelerate the association between PA and DNA, but the bulky size of TMG can cause steric hindrance and unfavourable repulsive electrostatic interactions in some PAs. The future design of stronger binding PA requires careful combination of βs and cationic substituents.
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Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
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Antony-Debré I, Paul A, Leite J, Mitchell K, Kim HM, Carvajal LA, Todorova TI, Huang K, Kumar A, Farahat AA, Bartholdy B, Narayanagari SR, Chen J, Ambesi-Impiombato A, Ferrando AA, Mantzaris I, Gavathiotis E, Verma A, Will B, Boykin DW, Wilson WD, Poon GM, Steidl U. Pharmacological inhibition of the transcription factor PU.1 in leukemia. J Clin Invest 2017; 127:4297-4313. [PMID: 29083320 DOI: 10.1172/jci92504] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Accepted: 09/21/2017] [Indexed: 11/17/2022] Open
Abstract
The transcription factor PU.1 is often impaired in patients with acute myeloid leukemia (AML). Here, we used AML cells that already had low PU.1 levels and further inhibited PU.1 using either RNA interference or, to our knowledge, first-in-class small-molecule inhibitors of PU.1 that we developed specifically to allosterically interfere with PU.1-chromatin binding through interaction with the DNA minor groove that flanks PU.1-binding motifs. These small molecules of the heterocyclic diamidine family disrupted the interaction of PU.1 with target gene promoters and led to downregulation of canonical PU.1 transcriptional targets. shRNA or small-molecule inhibition of PU.1 in AML cells from either PU.1lo mutant mice or human patients with AML-inhibited cell growth and clonogenicity and induced apoptosis. In murine and human AML (xeno)transplantation models, treatment with our PU.1 inhibitors decreased tumor burden and resulted in increased survival. Thus, our study provides proof of concept that PU.1 inhibition has potential as a therapeutic strategy for the treatment of AML and for the development of small-molecule inhibitors of PU.1.
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Affiliation(s)
- Iléana Antony-Debré
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Joana Leite
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kelly Mitchell
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Hye Mi Kim
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Luis A Carvajal
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Tihomira I Todorova
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | - Kenneth Huang
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Arvind Kumar
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Abdelbasset A Farahat
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA.,Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Boris Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Jiahao Chen
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA
| | | | - Adolfo A Ferrando
- Institute for Cancer Genetics, Columbia University, New York, New York, USA
| | - Ioannis Mantzaris
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA
| | - Evripidis Gavathiotis
- Department of Biochemistry.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Amit Verma
- Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - Britta Will
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Gregory Mk Poon
- Department of Chemistry, Georgia State University, Atlanta, Georgia, USA
| | - Ulrich Steidl
- Department of Cell Biology, Albert Einstein College of Medicine, New York, New York, USA.,Department of Medicine (Oncology), Division of Hemato-Oncology, Albert Einstein College of Medicine-Montefiore Medical Center, New York, New York, USA.,Albert Einstein Cancer Center, and.,Ruth L. and David S. Gottesman Institute for Stem Cell Biology and Regenerative Medicine, Albert Einstein College of Medicine, New York, New York, USA
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Abstract
Neuroblastoma is a cancer of the neural crest almost exclusively seen in childhood. While children with single, small primary tumors are often cured with surgery alone, the 65% of children with neuroblastoma whose disease has metastasized have less than a 50% chance of surviving five years after diagnosis. Innovative pharmacological strategies are critically needed for these children. Efforts to identify novel targets that afford ablation of neuroblastoma with minimal toxicity to normal tissues are underway. Developing approaches to neuroblastoma include those that target the catecholamine transporter, ubiquitin E3 ligase, the ganglioside GD2, the retinoic acid receptor, the protein kinases ALK and Aurora, and protein arginine N-methyltransferases. Here, as examples of the use of chemistry to combat neuroblastoma, we describe targeting of the protein arginine N-methyltransferases and their role in prolonging the half-life of the neuroblastoma oncoprotein N-Myc, redox signaling in neuroblastoma, and developmentally regulated proteins expressed in primitive neuroblastoma cells but not in mature neural crest elements.
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Affiliation(s)
- Jeanne N Hansen
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Xingguo Li
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Y George Zheng
- Department of Pharmaceutical and Biochemical Sciences, University of Georgia , Athens, Georgia 30602, United States
| | - Louis T Lotta
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Abhishek Dedhe
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Nina F Schor
- Department of Pediatrics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
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49
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Laughlin-Toth S, Carter EK, Ivanov I, Wilson WD. DNA microstructure influences selective binding of small molecules designed to target mixed-site DNA sequences. Nucleic Acids Res 2017; 45:1297-1306. [PMID: 28180310 PMCID: PMC5388402 DOI: 10.1093/nar/gkw1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Revised: 11/18/2016] [Accepted: 11/23/2016] [Indexed: 12/18/2022] Open
Abstract
Specific targeting of protein–nucleic acid interactions is an area of current interest, for example, in the regulation of gene-expression. Most transcription factor proteins bind in the DNA major groove; however, we are interested in an approach using small molecules to target the minor groove to control expression by an allosteric mechanism. In an effort to broaden sequence recognition of DNA-targeted-small-molecules to include both A·T and G·C base pairs, we recently discovered that the heterocyclic diamidine, DB2277, forms a strong monomer complex with a DNA sequence containing 5΄-AAAGTTT-3΄. Competition mass spectrometry and surface plasmon resonance identified new monomer complexes, as well as unexpected binding of two DB2277 with certain sequences. Inherent microstructural differences within the experimental DNAs were identified through computational analyses to understand the molecular basis for recognition. These findings emphasize the critical nature of the DNA minor groove microstructure for sequence-specific recognition and offer new avenues to design synthetic small molecules for effective regulation of gene-expression.
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Affiliation(s)
- Sarah Laughlin-Toth
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - E Kathleen Carter
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - Ivaylo Ivanov
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA, USA
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50
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Guo P, Paul A, Kumar A, Harika NK, Wang S, Farahat AA, Boykin DW, Wilson WD. A modular design for minor groove binding and recognition of mixed base pair sequences of DNA. Chem Commun (Camb) 2017; 53:10406-10409. [PMID: 28880316 PMCID: PMC5616130 DOI: 10.1039/c7cc06246j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The design and synthesis of compounds that target mixed, AT/GC, DNA sequences is described. The design concept connects two N-methyl-benzimidazole-thiophene single GC recognition units with a flexible linker that lets the compound fit the shape and twist of the DNA minor groove while covering a full turn of the double helix.
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Affiliation(s)
- Pu Guo
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Ananya Paul
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Arvind Kumar
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Narinder K Harika
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Siming Wang
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - Abdelbasset A Farahat
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - David W Boykin
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
| | - W David Wilson
- Department of Chemistry and Center for Diagnostics and Therapeutics Georgia State University, 50 Decatur St Se, Atlanta, GA 30303-3083, USA.
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