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Allen MD, Bycroft M, Zinzalla G. Structure of the BRK domain of the SWI/SNF chromatin remodeling complex subunit BRG1 reveals a potential role in protein-protein interactions. Protein Sci 2020; 29:1047-1053. [PMID: 31909846 PMCID: PMC7096718 DOI: 10.1002/pro.3820] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 12/31/2022]
Abstract
BRG1/SMARCA4 and its paralog BRM/SMARCA2 are the ATPase subunits of human SWI/SNF chromatin remodeling complexes. These multisubunit assemblies can act as either tumor suppressors or drivers of cancer, and inhibiting both BRG1 and BRM, is emerging as an effective therapeutic strategy in diverse cancers. BRG1 and BRM contain a BRK domain. The function of this domain is unknown, but it is often found in proteins involved in transcription and developmental signaling in higher eukaryotes, in particular in proteins that remodel chromatin. We report the NMR structure of the BRG1 BRK domain. It shows similarity to the glycine-tyrosine-phenylalanine (GYF) domain, an established protein-protein interaction module. Computational peptide-binding-site analysis of the BRK domain identifies a binding site that coincides with a highly conserved groove on the surface of the protein. This sets the scene for experiments to elucidate the role of this domain, and evaluate the potential of targeting it for cancer therapy.
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Affiliation(s)
- Mark D Allen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
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2
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Sammak S, Hamdani N, Gorrec F, Allen MD, Freund SMV, Bycroft M, Zinzalla G. Crystal Structures and Nuclear Magnetic Resonance Studies of the Apo Form of the c-MYC:MAX bHLHZip Complex Reveal a Helical Basic Region in the Absence of DNA. Biochemistry 2019; 58:3144-3154. [PMID: 31260268 PMCID: PMC6791285 DOI: 10.1021/acs.biochem.9b00296] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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The c-MYC transcription
factor is a master regulator of cell growth
and proliferation and is an established target for cancer therapy.
This basic helix–loop–helix Zip protein forms a heterodimer
with its obligatory partner MAX, which binds to DNA via the basic
region. Considerable research efforts are focused on targeting the
heterodimerization interface and the interaction of the complex with
DNA. The only available crystal structure is that of a c-MYC:MAX complex
artificially tethered by an engineered disulfide linker and prebound
to DNA. We have carried out a detailed structural analysis of the
apo form of the c-MYC:MAX complex, with no artificial linker, both
in solution using nuclear magnetic resonance (NMR) spectroscopy and
by X-ray crystallography. We have obtained crystal structures in three
different crystal forms, with resolutions between 1.35 and 2.2 Å,
that show extensive helical structure in the basic region. Determination
of the α-helical propensity using NMR chemical shift analysis
shows that the basic region of c-MYC and, to a lesser extent, that
of MAX populate helical conformations. We have also assigned the NMR
spectra of the c-MYC basic helix–loop–helix Zip motif
in the absence of MAX and showed that the basic region has an intrinsic
helical propensity even in the absence of its dimerization partner.
The presence of helical structure in the basic regions in the absence
of DNA suggests that the molecular recognition occurs via a conformational
selection rather than an induced fit. Our work provides both insight
into the mechanism of DNA binding and structural information to aid
in the development of MYC inhibitors.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Fabrice Gorrec
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark D Allen
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology , Cambridge Biomedical Campus , Francis Crick Avenue , Cambridge CB2 0QH , U.K
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
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Sammak S, Allen MD, Hamdani N, Bycroft M, Zinzalla G. The structure of INI1/hSNF5 RPT1 and its interactions with the c-MYC:MAX heterodimer provide insights into the interplay between MYC and the SWI/SNF chromatin remodeling complex. FEBS J 2018; 285:4165-4180. [PMID: 30222246 PMCID: PMC6398391 DOI: 10.1111/febs.14660] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/14/2018] [Indexed: 12/14/2022]
Abstract
c‐MYC and the SWI/SNF chromatin remodeling complex act as master regulators of transcription, and play a key role in human cancer. Although they are known to interact, the molecular details of their interaction are lacking. We have determined the structure of the RPT1 region of the INI1/hSNF5/BAF47/SMARCB1 subunit of the SWI/SNF complex that acts as a c‐MYC‐binding domain, and have localized the interaction regions on both INI1 and on the c‐MYC:MAX heterodimer. c‐MYC interacts with a highly conserved groove on INI1, while INI1 binds to the c‐MYC helix‐loop‐helix region. The binding site overlaps with the c‐MYC DNA‐binding region, and we show that binding of INI1 and E‐box DNA to c‐MYC:MAX are mutually exclusive.
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Affiliation(s)
- Susan Sammak
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark D Allen
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Najoua Hamdani
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Giovanna Zinzalla
- Microbiology, Tumor and Cell Biology (MTC) Department, Karolinska Institutet, Stockholm, Sweden
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4
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Castell A, Yan Q, Fawkner K, Hydbring P, Zhang F, Verschut V, Franco M, Zakaria SM, Bazzar W, Goodwin J, Zinzalla G, Larsson LG. A selective high affinity MYC-binding compound inhibits MYC:MAX interaction and MYC-dependent tumor cell proliferation. Sci Rep 2018; 8:10064. [PMID: 29968736 PMCID: PMC6030159 DOI: 10.1038/s41598-018-28107-4] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/22/2018] [Indexed: 02/07/2023] Open
Abstract
MYC is a key player in tumor development, but unfortunately no specific MYC-targeting drugs are clinically available. MYC is strictly dependent on heterodimerization with MAX for transcription activation. Aiming at targeting this interaction, we identified MYCMI-6 in a cell-based protein interaction screen for small inhibitory molecules. MYCMI-6 exhibits strong selective inhibition of MYC:MAX interaction in cells and in vitro at single-digit micromolar concentrations, as validated by split Gaussia luciferase, in situ proximity ligation, microscale thermophoresis and surface plasmon resonance (SPR) assays. Further, MYCMI-6 blocks MYC-driven transcription and binds selectively to the MYC bHLHZip domain with a KD of 1.6 ± 0.5 μM as demonstrated by SPR. MYCMI-6 inhibits tumor cell growth in a MYC-dependent manner with IC50 concentrations as low as 0.5 μM, while sparing normal cells. The response to MYCMI-6 correlates with MYC expression based on data from 60 human tumor cell lines and is abrogated by MYC depletion. Further, it inhibits MYC:MAX interaction, reduces proliferation and induces massive apoptosis in tumor tissue from a MYC-driven xenograft tumor model without severe side effects. Since MYCMI-6 does not affect MYC expression, it is a unique molecular tool to specifically target MYC:MAX pharmacologically and it has good potential for drug development.
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Affiliation(s)
- Alina Castell
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Qinzi Yan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Karin Fawkner
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
- TLV, Box 225 20, 104 22, Stockholm, Sweden
| | - Per Hydbring
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
- Department of Oncology-Pathology, Karolinska Institutet, SE-17176, Stockholm, Sweden
| | - Fan Zhang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Vasiliki Verschut
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Marcela Franco
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Siti Mariam Zakaria
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Wesam Bazzar
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Jacob Goodwin
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Giovanna Zinzalla
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden
| | - Lars-Gunnar Larsson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-171 65, Stockholm, Sweden.
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Castell A, Yan Q, Fawkner K, Hydbring P, Zhang F, Verschut V, Franco M, Zinzalla G, Larsson LG. Abstract 3952: Selective high affinity MYC-binding compound inhibits MYC-MAX interaction and MYC-dependent tumor cell growth. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The MYC family oncoproteins/transcription factors MYC, MYCN and MYCL (here referred to as MYC) are key players in tumor development and are particularly associated with aggressive disease and poor prognosis. Efficient and specific MYC-targeting drugs are therefore highly warranted, but no such drugs are available in the clinic at present. MYC is strictly dependent on heterodimerization with MAX for activation of transcription. In a cell-based Bimolecular Fluorescence Complementation protein-protein interaction screen for small molecule inhibitors we identified a molecule that exhibits strong selective inhibition of MYC-MAX interaction in cells as validated by Gaussia luciferase protein complementation assay, coimmunoprecipitation and in situ proximity ligation (isPLA) assay, reaching an IC50 at single-digit micromolar concentrations. The molecule was shown to inhibit MYC-MAX interactions in a biochemical FRET assay and binds selectively to the MYC bHLHZip domain with affinity in the single digit micromolar range as demonstrated by Microscale Thermophoresis and Surface Plasmon Resonance. Further, within the same concentration range, this molecule blocks MYC-driven transcription and efficiently inhibits tumor cell growth in a MYC-dependent manner, but spares normal cells. Moreover, the growth inhibitory responses to the molecule correlated significantly with MYC expression levels in a cohort of 60 human tumor cell lines. Importantly, utilizing a mouse tumor model of MYCN-amplified neuroblastoma, treatment with the molecule resulted in significant inhibition of the MYC-MAX interaction in tumor tissue, as shown by isPLA, and massive induction of apoptosis in the tumors. Since this molecule, unlike many experimental MYC inhibitors, is selective, has high affinity for MYC, has high efficacy in cells, reaches its target in vivo and does not affect MYC expression levels, it can be used as a chemical tool to specifically study the role of the MYC-MAX complex in MYC biology in normal and cancerous cells, and it has potential for drug development.
Citation Format: Alina Castell, Qinzi Yan, Karin Fawkner, Per Hydbring, Fan Zhang, Vasiliki Verschut, Marcela Franco, Giovanna Zinzalla, Lars-Gunnar Larsson. Selective high affinity MYC-binding compound inhibits MYC-MAX interaction and MYC-dependent tumor cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3952.
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Affiliation(s)
| | - Qinzi Yan
- Karolinska Institutet, Stockholm, Sweden
| | | | | | - Fan Zhang
- Karolinska Institutet, Stockholm, Sweden
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6
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Abstract
Mutations in subunits of the SWI/SNF chromatin remodelling complex are found in 20 % of human cancers. At face value, this would appear to indicate that this multiprotein complex is a potent tumour suppressor. However, it has recently emerged that some mutations in the SWI/SNF complex can have a gain-of-function effect and that in other tumours, such as pancreatic cancer, leukaemia, and breast cancer, the wild-type complex is used to drive cancer. Thus, paradoxically, this "tumour suppressor" has become an attractive target for developing anticancer agents. The SWI/SNF complex makes several protein-protein interactions both within the complex and with a wide range of transcription factors, and targeting these protein-protein interactions is emerging as the best approach to modulating the activity of the complex selectively.
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Affiliation(s)
- Giovanna Zinzalla
- Microbiology, Tumour and Cell Biology (MTC), and Science for Life Laboratory (SciLifeLab), Karolinska Institutet, Tomtebodavägen 23A, Stockholm, 171 65, Sweden.
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Sammak S, Zinzalla G. Targeting protein-protein interactions (PPIs) of transcription factors: Challenges of intrinsically disordered proteins (IDPs) and regions (IDRs). Prog Biophys Mol Biol 2015; 119:41-6. [PMID: 26126425 DOI: 10.1016/j.pbiomolbio.2015.06.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2015] [Revised: 06/23/2015] [Accepted: 06/25/2015] [Indexed: 12/26/2022]
Abstract
In this review we discuss recent progress in targeting the protein-protein interactions made by oncogenic transcription factors. We particularly focus on the challenges posed by the prevalence of intrinsically disordered regions in this class of protein and the strategies being used to overcome them.
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Affiliation(s)
- Susan Sammak
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden
| | - Giovanna Zinzalla
- Department of Microbiology, Cell and Tumour Biology, and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23A, Stockholm 171 65, Sweden.
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8
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Allen MD, Freund SMV, Zinzalla G, Bycroft M. The SWI/SNF Subunit INI1 Contains an N-Terminal Winged Helix DNA Binding Domain that Is a Target for Mutations in Schwannomatosis. Structure 2015; 23:1344-9. [PMID: 26073604 PMCID: PMC4509781 DOI: 10.1016/j.str.2015.04.021] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Revised: 04/20/2015] [Accepted: 04/23/2015] [Indexed: 12/16/2022]
Abstract
SWI/SNF complexes use the energy of ATP hydrolysis to remodel chromatin. In mammals they play a central role in regulating gene expression during differentiation and proliferation. Mutations in SWI/SNF subunits are among the most frequent gene alterations in cancer. The INI1/hSNF5/SMARCB1 subunit is mutated in both malignant rhabdoid tumor, a highly aggressive childhood cancer, and schwannomatosis, a tumor-predisposing syndrome characterized by mostly benign tumors of the CNS. Here, we show that mutations in INI1 that cause schwannomatosis target a hitherto unidentified N-terminal winged helix DNA binding domain that is also present in the BAF45a/PHF10 subunit of the SWI/SNF complex. The domain is structurally related to the SKI/SNO/DAC domain, which is found in a number of metazoan chromatin-associated proteins. INI1 and its metazoan homologs contain a variant winged helix DNA binding domain A homologous domain is present in the BAF45a/PHF10 subunit of the SWI/SNF complex Structurally related domains are found in other metazoan chromatin-associated proteins INI1 mutations that cause schwannomatosis map to the winged helix domain
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Affiliation(s)
- Mark D Allen
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Stefan M V Freund
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Giovanna Zinzalla
- Centre for Advanced Cancer Therapies, Department of Microbiology, Cell and Tumour Biology and Science for Life Laboratory, Karolinska Institutet, Tomtebodavägen 23, Stockholm 171 65, Sweden
| | - Mark Bycroft
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK.
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Bendiabdellah Y, Rahman KM, Uranchimeg B, Nahar KS, Antonow D, Shoemaker RH, Melillo G, Zinzalla G, Thurston DE. Tetracycline analogues with a selective inhibitory effect on HIF-1α. Med Chem Commun 2014. [DOI: 10.1039/c4md00111g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Nkansah E, Shah R, Collie GW, Parkinson GN, Palmer J, Rahman KM, Bui TT, Drake AF, Husby J, Neidle S, Zinzalla G, Thurston DE, Wilderspin AF. Observation of unphosphorylated STAT3 core protein binding to targetdsDNA by PEMSA and X-ray crystallography. FEBS Lett 2013; 587:833-9. [DOI: 10.1016/j.febslet.2013.01.065] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Revised: 01/17/2013] [Accepted: 01/24/2013] [Indexed: 10/27/2022]
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Harvey SR, Porrini M, Stachl C, MacMillan D, Zinzalla G, Barran PE. Small-molecule inhibition of c-MYC:MAX leucine zipper formation is revealed by ion mobility mass spectrometry. J Am Chem Soc 2012; 134:19384-92. [PMID: 23106332 DOI: 10.1021/ja306519h] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The leucine zipper interaction between MAX and c-MYC has been studied using mass spectrometry and drift time ion mobility mass spectrometry (DT IM-MS) in addition to circular dichroism spectroscopy. Peptides comprising the leucine zipper sequence with (c-MYC-Zip residues 402-434) and without a postulated small-molecule binding region (c-MYC-ZipΔDT residues 406-434) have been synthesized, along with the corresponding MAX leucine zipper (MAX-Zip residues 74-102). c-MYC-Zip:MAX-Zip complexes are observed both in the absence and in the presence of the reported small-molecule inhibitor 10058-F4 for both forms of c-MYC-Zip. DT IM-MS, in combination with molecular dynamics (MD), shows that the c-MYC-Zip:MAX-Zip complex [M+5H](5+) exists in two conformations, one extended with a collision cross section (CCS) of 1164 ± 9.3 Å(2) and one compact with a CCS of 982 ± 6.6 Å(2); similar values are observed for the two forms of c-MYC-ZipΔDT:MAX-Zip. Candidate geometries for the complexes have been evaluated with MD simulations. The helical leucine zipper structure previously determined from NMR measurements (Lavigne, P.; et al. J. Mol. Biol. 1998, 281, 165), altered to include the DT region and subjected to a gas-phase minimization, yields a CCS of 1247 Å(2), which agrees with the extended conformation we observe experimentally. More extensive MD simulations provide compact complexes which are found to be highly disordered, with CCSs that correspond to the compact form from experiment. In the presence of the ligand, the leucine zipper conformation is completely inhibited and only the more disordered species is observed, providing a novel method to study the effect of interactions of disordered systems and subsequent inhibition of the formation of an ordered helical complex.
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Affiliation(s)
- Sophie R Harvey
- EastChem School of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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Husby J, Todd AK, Haider SM, Zinzalla G, Thurston DE, Neidle S. Molecular dynamics studies of the STAT3 homodimer:DNA complex: relationships between STAT3 mutations and protein-DNA recognition. J Chem Inf Model 2012; 52:1179-92. [PMID: 22500887 DOI: 10.1021/ci200625q] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Signal Transducers and Activators of Transcription (STAT) proteins are a group of latent cytoplasmic transcription factors involved in cytokine signaling. STAT3 is a member of the STAT family and is expressed at elevated levels in a large number of diverse human cancers and is now a validated target for anticancer drug discovery.. Understanding the dynamics of the STAT3 dimer interface, accounting for both protein-DNA and protein-protein interactions, with respect to the dynamics of the latent unphosphorylated STAT3 monomer, is important for designing potential small-molecule inhibitors of the activated dimer. Molecular dynamics (MD) simulations have been used to study the activated STAT3 homodimer:DNA complex and the latent unphosphorylated STAT3 monomer in an explicit water environment. Analysis of the data obtained from MD simulations over a 50 ns time frame has suggested how the transcription factor interacts with DNA, the nature of the conformational changes, and ways in which function may be affected. Examination of the dimer interface, focusing on the protein-DNA interactions, including involvement of water molecules, has revealed the key residues contributing to the recognition events involved in STAT3 protein-DNA interactions. This has shown that the majority of mutations in the DNA-binding domain are found at the protein-DNA interface. These mutations have been mapped in detail and related to specific protein-DNA contacts. Their structural stability is described, together with an analysis of the model as a starting-point for the discovery of novel small-molecule STAT3 inhibitors.
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Affiliation(s)
- Jarmila Husby
- CRUK Biomolecular Structure Group, UCL School of Pharmacy, University College London, WC1N 1AX London, UK
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Zinzalla G, Bendiabdellah Y, Villanueva-Margalef I, Misale A, Nahar K, Haque M, Thurston [. One-Pot Synthesis of Fused-Tetracyclic Scaffolds Employing a Lewis Acid Promoted Domino Reaction of Naphthoquinones. SYNTHESIS-STUTTGART 2011. [DOI: 10.1055/s-0030-1260073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Rahman KM, Palmer J, Essex S, Nkansah E, Zinzalla G, Wilderspin AF, Bui TT, Drake AF, Thurston DE. Abstract 1382: Use of polarized light spectroscopy (CD) to study STAT3 folding and STAT3:ligand interactions. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-1382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
STAT3 is a homodimeric transcription factor that is over-expressed in variety of solid tumours. It is known to trigger transcription of a range of genes associated with tumour growth and metastasis. In order to use the STAT3/STAT3 dimer for drug discovery, the factors affecting dimerisation of the monomeric protein and the interaction with ligands must be understood. In this study, we have demonstrated that Circular Dichroism (CD) can be used as a tool to study these processes. We have found that formation of the dimeric STAT3/STAT3 complex results in an induced CD signal which is absent in monomeric protein. Thus, CD can be used to optimize conditions for the production and storage of un-phosphorylated (un-P-) and phosphorylated (P-) STAT3. A similar induced signal was observed when a small molecule (or peptide ligand) interacted with either un-P- or P-STAT3 due to chiral perturbation of the protein structure or electron rearrangements. Crucially, the intensity of the induced CD signal was found to depend on the strength and geometry of the interaction of the binding partner. CD was also used to determine the secondary structure of un-P- and P-STAT3. HIS- and FLAG-tagged STAT3 were examined using the far-UV spectral region (190-250 nm), and the regular folded environment of the peptidic bonds was used to determine the alpha-helix, beta-sheet, and random coil content of different batches of STAT3 protein. For batches of P-STAT3, the composition was found to be 28.3% α-helix, 22.3% β-sheet and 49.4% random coils. For un-P-STAT3, the β-sheet content was slightly higher (23.2%) while the α-helix content was lower (26.8%). Next, protein:ligand interactions which alter the conformation of the protein were studied. Titration of un-P-STAT monomer with different small-molecule inhibitors produced a significant change in the CD spectrum consistent with modification of secondary structure due to altered folding. In particular, significant effects on the secondary structures of both un-P- and P-STAT3 were observed upon binding of the natural peptidic ligands LKTKF and LPQTV. Crucially, the different complex geometries adopted by the proteins upon interaction with ligands could be used to determine the stoichiometry of interaction and the orientation of the ligands in the binding pocket of the protein. These results demonstrate that CD spectroscopy can be used to evaluate STAT3 structure and ligand interactions at the molecular level, and thus represents a useful analytical tool in the development of small molecule inhibitors for potential therapeutic use.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1382. doi:10.1158/1538-7445.AM2011-1382
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Affiliation(s)
- Khondaker M. Rahman
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Jonathan Palmer
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Samantha Essex
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Edwin Nkansah
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Giovanna Zinzalla
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Andrew F. Wilderspin
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Tam T.T Bui
- 2Biomolecular Spectroscopy Centre, Kings College London, Guy's Campus, London, SE1 1UL, United Kingdom
| | - Alex F. Drake
- 2Biomolecular Spectroscopy Centre, Kings College London, Guy's Campus, London, SE1 1UL, United Kingdom
| | - David E. Thurston
- 1CR-UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
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Zinzalla G, Haque MR, Piku Basu B, Anderson J, Kaye SL, Haider S, Hasan F, Antonow D, Essex S, Rahman KM, Palmer J, Morgenstern D, Wilderspin AF, Neidle S, Thurston DE. A novel small-molecule inhibitor of IL-6 signalling. Bioorg Med Chem Lett 2010; 20:7029-32. [DOI: 10.1016/j.bmcl.2010.09.117] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2010] [Revised: 09/21/2010] [Accepted: 09/23/2010] [Indexed: 01/05/2023]
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Haque MR, Zinzalla G, Kaye SL, Haider S, Basu BP, Anderson J, Rahman KM, Antonow D, Essex S, Palmer J, Nkansah E, Hasan F, Morgenstern D, Wilderspin AF, Neidle S, Thurston DE. Abstract 5454: Novel STAT3:STAT3 small-molecule inhibitors as potential anticancer agents. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-5454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Transcription factors are important targets for cancer therapy. The inhibition of protein-protein interactions (PPIs) within signalling pathways known to be key regulators of transcriptional activity is a viable approach to novel chemotherapeutic strategies. Proof-of-concept studies in cell-culture and animal models have validated the potential of small-molecule inhibitors of STAT3 signalling in cancer therapy. In particular, the protein-protein interaction between two STAT3 monomers (i.e., the dimerisation event in the signalling cascade) has been identified as a valid target to inhibit DNA-binding and the resultant transcriptional activation. Of the approximately 20 small-molecule STAT3 inhibitors reported in the literature to date, only three are described as potential STAT3:STAT3 dimerisation inhibitors, and these have IC50 values in STAT3-expressing cell lines of between 10-90 μM.
Using in silico and medicinal chemistry-based approaches based on a published X-Ray structure of STAT3 (PDB: ID-1BG1) to identify “hit” inhibitors, a focussed library (approx. 50 members) was designed around one such “hit” and synthesized employing an efficient 4-step linear approach. Library members were then entered into a screening cascade involving initial evaluation of their ability to inhibit STAT3:STAT3 interaction in a Fluorescent Polarisation (FP)-based primary PPI binding assay. “Hit” molecules from this primary assay were then studied in two cell-based assays designed to test for STAT3 selectivity. The first was a comparative MTS assay between STAT3-expressing MDA MB231 breast cancer cells and STAT3-null colon A4 cells. The second was a luciferase reporter assay designed to measure transcription inhibition in STAT3-Luc-transformed Hela cells compared to SV40-Luc-transformed Hela control cells. A potential “lead” molecule, RH06, emerged from this screening cascade with potentially selective STAT3 inhibitory activity in the low micromolar (i.e., ∼1 µM) region. RH06 is currently being studied for its effect on STAT3 and pSTAT3 signal activation, and its potentially differential effect on upstream and downstream mediators (i.e., JAK2, Bcl-xl, Cyclin D1 and pSTAT1).
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 5454.
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Affiliation(s)
- Mohammad R. Haque
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Giovanna Zinzalla
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Samantha L. Kaye
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Shozeb Haider
- 2Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - B. Piku Basu
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - John Anderson
- 3UCL Institute of Child Health, London, United Kingdom
| | - Khondaker M. Rahman
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Dyeison Antonow
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Samantha Essex
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Jonathan Palmer
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Edwin Nkansah
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Fyeza Hasan
- 3UCL Institute of Child Health, London, United Kingdom
| | | | - Andrew F. Wilderspin
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - Stephen Neidle
- 2Cancer Research UK Biomolecular Structure Group, The School of Pharmacy, Univ. of London, London, United Kingdom
| | - David E. Thurston
- 1Cancer Research UK Protein-Protein Interactions Drug Discovery Research Group, The School of Pharmacy, Univ. of London, London, United Kingdom
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Antonow D, Marrafa T, Dawood I, Ahmed T, Haque MR, Thurston DE, Zinzalla G. Facile oxidation of electron-poor benzo[b]thiophenes to the corresponding sulfones with an aqueous solution of H2O2 and P2O5. Chem Commun (Camb) 2010; 46:2289-91. [DOI: 10.1039/b924333j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Villanueva-Margalef I, Thurston DE, Zinzalla G. Facile nucleophilic substitution at the C3a tertiary carbon of the 3a-bromohexahydropyrrolo[2,3-b]indole scaffold. Org Biomol Chem 2010; 8:5294-303. [DOI: 10.1039/c0ob00327a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Milroy LG, Zinzalla G, Loiseau F, Qian Z, Prencipe G, Pepper C, Fegan C, Ley S. Natural-Product-Like Spiroketals and Fused Bicyclic Acetals as Potential Therapeutic Agents for B-Cell Chronic Lymphocytic Leukaemia. ChemMedChem 2008; 3:1922-35. [DOI: 10.1002/cmdc.200800265] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Milroy LG, Zinzalla G, Prencipe G, Michel P, Ley S, Gunaratnam M, Beltran M, Neidle S. Chemical Variation of Natural-Product-Like Scaffolds: Design, Synthesis, and Biological Activity of Fused Bicyclic Acetal Derivatives. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604688] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Milroy LG, Zinzalla G, Prencipe G, Michel P, Ley SV, Gunaratnam M, Beltran M, Neidle S. Chemical Variation of Natural-Product-Like Scaffolds: Design, Synthesis, and Biological Activity of Fused Bicyclic Acetal Derivatives. Angew Chem Int Ed Engl 2007; 46:2493-6. [PMID: 17318936 DOI: 10.1002/anie.200604688] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Lech-Gustav Milroy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK
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Abstract
The design and synthesis of spiroketal structures and their chemical modification, leading to a collection of new small molecules for biological evaluation as orally-bioavailable lead compounds is described. Both [6,5]- and [6,6]-membered ring spiroketal units have been prepared in a stereochemically-varying fashion starting from commercially available (R)- or (S)-glycidol, in ten, eleven and twelve linear steps, in overall yields of 45, 40 and 20%, respectively. Further elaboration according to Lipinski's guidelines has given a collection of structurally-diverse, new spiroketal derivatives in high yields and with high purity.
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Affiliation(s)
- Giovanna Zinzalla
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, UK CB2 1EW
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23
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Baldoli C, Falciola L, Licandro E, Maiorana S, Mussini P, Ramani P, Rigamonti C, Zinzalla G. Erratum to “A new ferrocene conjugate of a tyrosine PNA monomer: synthesis and electrochemical properties” [J. Organomet. Chem. 689 (25) (2004) 4791]. J Organomet Chem 2006. [DOI: 10.1016/j.jorganchem.2005.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Baldoli C, Falciola L, Licandro E, Maiorana S, Mussini P, Ramani P, Rigamonti C, Zinzalla G. A new ferrocene conjugate of a tyrosine PNA monomer: synthesis and electrochemical properties. J Organomet Chem 2004. [DOI: 10.1016/j.jorganchem.2004.09.049] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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25
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Baldoli C, Maiorana S, Giannini C, Licandro E, Zinzalla G. A Thymine-PNA Monomer as New Isocyanide Component in the Ugi Reaction: A Direct Entry to PNA Dimers. Synlett 2004. [DOI: 10.1055/s-2004-822886] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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26
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Baldoli C, Maiorana S, Licandro E, Casiraghi L, Zinzalla G, Seneci P, De Magistris E, Paio A, Marchioro C. Polymer-Supported Haloarene Chromium Dicarbonyl Isonitrile Complexes: A Study of Their Synthesis and Reactivity. ACTA ACUST UNITED AC 2003; 5:809-13. [PMID: 14606809 DOI: 10.1021/cc0340123] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Different arene Cr(CO)(3) complexes were supported on a polystyrene isonitrile resin by photochemical-promoted replacement of a chromium carbonyl ligand by the NC group. The supported complexes proved to be stable and were successfully used for further transformations. In particular, the reactivity of dichlorobenzene complexes to different nucleophiles was investigated and found to be comparable with that of the parent Cr(CO)(3) complexes.
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Affiliation(s)
- Clara Baldoli
- Dipartimento di Chimica Organica e Industriale, Istituto di Scienze e Tecnologie Molecolari, Centro di Eccellenza CISI, University of Milan and CNR, Via C. Golgi 19, I-20133 Milan, Italy.
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27
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Baldoli C, Maiorana S, Licandro E, Zinzalla G, Perdicchia D. Synthesis of chiral chromium tricarbonyl labeled thymine PNA monomers via the Ugi reaction. Org Lett 2002; 4:4341-4. [PMID: 12443093 DOI: 10.1021/ol026994a] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Ugi condensation was used to synthesize the first examples of chiral racemic Ar.Cr(CO)(3) labeled peptide nucleic acid (PNA) monomers bearing the organometallic moiety linked to the alpha-carbon of the glycine unit.
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Affiliation(s)
- Clara Baldoli
- CNR Istituto di Scienze e Tecnologie Molecolari e Dipartimento di Chimica Organica e Industriale, University of Milan, Via C. Golgi 19, I-20133 Milano, Italy
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28
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Baldoli C, Maiorana S, Licandro E, Zinzalla G, Lanfranchi M, Tiripicchio A. Stereoselective hetero Diels–Alder reactions of chiral tricarbonyl (η6-benzaldehyde)chromium complexes. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0957-4166(01)00347-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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