1
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Ren L, Zhang T, Zhang J. Recent advances in dietary androgen receptor inhibitors. Med Res Rev 2024; 44:1446-1500. [PMID: 38279967 DOI: 10.1002/med.22019] [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: 10/20/2022] [Revised: 12/07/2023] [Accepted: 01/10/2024] [Indexed: 01/29/2024]
Abstract
As a nuclear transcription factor, the androgen receptor (AR) plays a crucial role not only in normal male sexual differentiation and growth of the prostate, but also in benign prostatic hyperplasia, prostatitis, and prostate cancer. Multiple population-based epidemiological studies demonstrated that prostate cancer risk was inversely associated with increased dietary intakes of green tea, soy products, tomato, and so forth. Therefore, this review aimed to summarize the structure and function of AR, and further illustrate the structural basis for antagonistic mechanisms of the currently clinically available antiandrogens. Due to the limitations of these antiandrogens, a series of natural AR inhibitors have been identified from edible plants such as fruits and vegetables, as well as folk medicines, health foods, and nutritional supplements. Hence, this review mainly focused on recent experimental, epidemiological, and clinical studies about natural AR inhibitors, particularly the association between dietary intake of natural antiandrogens and reduced risk of prostatic diseases. Since natural products offer multiple advantages over synthetic antiandrogens, this review may provide a comprehensive and updated overview of dietary-derived AR inhibitors, as well as their potential for the nutritional intervention against prostatic disorders.
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Affiliation(s)
- Li Ren
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, China
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2
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Xiang T, Shi C, Guo Y, Zhang J, Min W, Sun J, Liu J, Yan X, Liu Y, Yao L, Mao Y, Yang X, Shi J, Yan B, Qu G, Jiang G. Effect-directed analysis of androgenic compounds from sewage sludges in China. WATER RESEARCH 2024; 256:121652. [PMID: 38657313 DOI: 10.1016/j.watres.2024.121652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 04/16/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
The safety of municipal sewage sludge has raised great concerns because of the accumulation of large-scale endocrine disrupting chemicals in the sludge during wastewater treatment. The presence of contaminants in sludge can cause secondary pollution owing to inappropriate disposal mechanisms, posing potential risks to the environment and human health. Effect-directed analysis (EDA), involving an androgen receptor (AR) reporter gene bioassay, fractionation, and suspect and nontarget chemical analysis, were applied to identify causal AR agonists in sludge; 20 of the 30 sludge extracts exhibited significant androgenic activity. Among these, the extracts from Yinchuan, Kunming, and Shijiazhuang, which held the most polluted AR agonistic activities were prepared for extensive EDA, with the dihydrotestosterone (DHT)-equivalency of 2.5 - 4.5 ng DHT/g of sludge. Seven androgens, namely boldione, androstenedione, testosterone, megestrol, progesterone, and testosterone isocaproate, were identified in these strongest sludges together, along with testosterone cypionate, first reported in sludge media. These identified androgens together accounted for 55 %, 87 %, and 52 % of the effects on the sludge from Yinchuan, Shijiazhuang, and Kunming, respectively. This study elucidates the causative androgenic compounds in sewage sludge and provides a valuable reference for monitoring and managing androgens in wastewater treatment.
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Affiliation(s)
- Tongtong Xiang
- College of Sciences, Northeastern University, Shenyang 110004, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Chunzhen Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; Department of Environmental Science and Engineering, Beijing Technology and Business University, Beijing 100048, China.
| | - Yunhe Guo
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China
| | - Jie Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Weicui Min
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Jiazheng Sun
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Jifu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
| | - Xiliang Yan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Yanna Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Linlin Yao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuxiang Mao
- School of Resources & Environment, Henan Polytechnic University, Jiaozuo 454000, China
| | - Xiaoxi Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China.
| | - Jianbo Shi
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environmental Studies, China University of Geosciences, Wuhan 430074, China
| | - Bing Yan
- School of Environmental Science and Engineering, Shandong University, Qingdao 266237, China; Institute of Environmental Research at Greater Bay Area, Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, Guangzhou University, Guangzhou 510006, China
| | - Guangbo Qu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
| | - Guibin Jiang
- College of Sciences, Northeastern University, Shenyang 110004, China; State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058, China; School of Environment, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310000, China
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Roggia M, Natale B, Amendola G, Di Maro S, Cosconati S. Streamlining Large Chemical Library Docking with Artificial Intelligence: the PyRMD2Dock Approach. J Chem Inf Model 2024; 64:2143-2149. [PMID: 37552222 PMCID: PMC11005044 DOI: 10.1021/acs.jcim.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Indexed: 08/09/2023]
Abstract
The present contribution introduces a novel computational protocol called PyRMD2Dock, which combines the Ligand-Based Virtual Screening (LBVS) tool PyRMD with the popular docking software AutoDock-GPU (AD4-GPU) to enhance the throughput of virtual screening campaigns for drug discovery. By implementing PyRMD2Dock, we demonstrate that it is possible to rapidly screen massive chemical databases and identify those with the highest predicted binding affinity to a target protein. Our benchmarking and screening experiments illustrate the predictive power and speed of PyRMD2Dock and highlight its potential to accelerate the discovery of novel drug candidates. Overall, this study showcases the value of combining AI-powered LBVS tools with docking software to enable effective and high-throughput virtual screening of ultralarge molecular databases in drug discovery. PyRMD and the PyRMD2Dock protocol are freely available on GitHub (https://github.com/cosconatilab/PyRMD) as an open-source tool.
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Affiliation(s)
- Michele Roggia
- DiSTABiF, University
of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Benito Natale
- DiSTABiF, University
of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Giorgio Amendola
- DiSTABiF, University
of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Salvatore Di Maro
- DiSTABiF, University
of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
| | - Sandro Cosconati
- DiSTABiF, University
of Campania Luigi Vanvitelli, Via Vivaldi 43, 81100 Caserta, Italy
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4
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Popov KI, Wellnitz J, Maxfield T, Tropsha A. HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra-large chemical libraries. Mol Inform 2024; 43:e202300207. [PMID: 37802967 PMCID: PMC11156482 DOI: 10.1002/minf.202300207] [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: 08/16/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/08/2023]
Abstract
Recent rapid expansion of make-on-demand, purchasable, chemical libraries comprising dozens of billions or even trillions of molecules has challenged the efficient application of traditional structure-based virtual screening methods that rely on molecular docking. We present a novel computational methodology termed HIDDEN GEM (HIt Discovery using Docking ENriched by GEnerative Modeling) that greatly accelerates virtual screening. This workflow uniquely integrates machine learning, generative chemistry, massive chemical similarity searching and molecular docking of small, selected libraries in the beginning and the end of the workflow. For each target, HIDDEN GEM nominates a small number of top-scoring virtual hits prioritized from ultra-large chemical libraries. We have benchmarked HIDDEN GEM by conducting virtual screening campaigns for 16 diverse protein targets using Enamine REAL Space library comprising 37 billion molecules. We show that HIDDEN GEM yields the highest enrichment factors as compared to state of the art accelerated virtual screening methods, while requiring the least computational resources. HIDDEN GEM can be executed with any docking software and employed by users with limited computational resources.
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Affiliation(s)
- Konstantin I. Popov
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- These authors contributed equally: Konstantin I. Popov, James Wellnitz, Travis Maxfield
| | - James Wellnitz
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- These authors contributed equally: Konstantin I. Popov, James Wellnitz, Travis Maxfield
| | - Travis Maxfield
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
- These authors contributed equally: Konstantin I. Popov, James Wellnitz, Travis Maxfield
| | - Alexander Tropsha
- UNC Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
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5
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Fancher AT, Hua Y, Close DA, Xu W, McDermott LA, Strock CJ, Santiago U, Camacho CJ, Johnston PA. Characterization of allosteric modulators that disrupt androgen receptor co-activator protein-protein interactions to alter transactivation-Drug leads for metastatic castration resistant prostate cancer. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:325-343. [PMID: 37549772 DOI: 10.1016/j.slasd.2023.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/06/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Three series of compounds were prioritized from a high content screening campaign that identified molecules that blocked dihydrotestosterone (DHT) induced formation of Androgen Receptor (AR) protein-protein interactions (PPIs) with the Transcriptional Intermediary Factor 2 (TIF2) coactivator and also disrupted preformed AR-TIF2 PPI complexes; the hydrobenzo-oxazepins (S1), thiadiazol-5-piperidine-carboxamides (S2), and phenyl-methyl-indoles (S3). Compounds from these series inhibited AR PPIs with TIF2 and SRC-1, another p160 coactivator, in mammalian 2-hybrid assays and blocked transcriptional activation in reporter assays driven by full length AR or AR-V7 splice variants. Compounds inhibited the growth of five prostate cancer cell lines, with many exhibiting differential cytotoxicity towards AR positive cell lines. Representative compounds from the 3 series substantially reduced both endogenous and DHT-enhanced expression and secretion of the prostate specific antigen (PSA) cancer biomarker in the C4-2 castration resistant prostate cancer (CRPC) cell line. The comparatively weak activities of series compounds in the H3-DHT and/or TIF2 box 3 LXXLL-peptide binding assays to the recombinant ligand binding domain of AR suggest that direct antagonism at the orthosteric ligand binding site or AF-2 surface respectively are unlikely mechanisms of action. Cellular enhanced thermal stability assays (CETSA) indicated that compounds engaged AR and reduced the maximum efficacy and right shifted the EC50 of DHT-enhanced AR thermal stabilization consistent with the effects of negative allosteric modulators. Molecular docking of potent representative hits from each series to AR structures suggest that S1-1 and S2-6 engage a novel binding pocket (BP-1) adjacent to the orthosteric ligand binding site, while S3-11 occupies the AR binding function 3 (BF-3) allosteric pocket. Hit binding poses indicate spaces and residues adjacent to the BP-1 and BF-3 pockets that will be exploited in future medicinal chemistry optimization studies. Small molecule allosteric modulators that prevent/disrupt AR PPIs with coactivators like TIF2 to alter transcriptional activation in the presence of orthosteric agonists might evade the resistance mechanisms to existing prostate cancer drugs and provide novel starting points for medicinal chemistry lead optimization and future development into therapies for metastatic CRPC.
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Affiliation(s)
- Ashley T Fancher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; Nucleus Global, 2 Ravinia Drive, Suite 605, Atlanta, GA 30346, USA
| | - Yun Hua
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - David A Close
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Wei Xu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lee A McDermott
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; PsychoGenics Inc, 215 College Road, Paramus, NJ 07652, USA
| | | | - Ulises Santiago
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, School of Medicine, at the University of Pittsburgh, USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, PA 15261, USA; University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA 15232, USA.
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6
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Tsai JM, Aguirre JD, Li YD, Brown J, Focht V, Kater L, Kempf G, Sandoval B, Schmitt S, Rutter JC, Galli P, Sandate CR, Cutler JA, Zou C, Donovan KA, Lumpkin RJ, Cavadini S, Park PMC, Sievers Q, Hatton C, Ener E, Regalado BD, Sperling MT, Słabicki M, Kim J, Zon R, Zhang Z, Miller PG, Belizaire R, Sperling AS, Fischer ES, Irizarry R, Armstrong SA, Thomä NH, Ebert BL. UBR5 forms ligand-dependent complexes on chromatin to regulate nuclear hormone receptor stability. Mol Cell 2023; 83:2753-2767.e10. [PMID: 37478846 PMCID: PMC11134608 DOI: 10.1016/j.molcel.2023.06.028] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 04/24/2023] [Accepted: 06/22/2023] [Indexed: 07/23/2023]
Abstract
Nuclear hormone receptors (NRs) are ligand-binding transcription factors that are widely targeted therapeutically. Agonist binding triggers NR activation and subsequent degradation by unknown ligand-dependent ubiquitin ligase machinery. NR degradation is critical for therapeutic efficacy in malignancies that are driven by retinoic acid and estrogen receptors. Here, we demonstrate the ubiquitin ligase UBR5 drives degradation of multiple agonist-bound NRs, including the retinoic acid receptor alpha (RARA), retinoid x receptor alpha (RXRA), glucocorticoid, estrogen, liver-X, progesterone, and vitamin D receptors. We present the high-resolution cryo-EMstructure of full-length human UBR5 and a negative stain model representing its interaction with RARA/RXRA. Agonist ligands induce sequential, mutually exclusive recruitment of nuclear coactivators (NCOAs) and UBR5 to chromatin to regulate transcriptional networks. Other pharmacological ligands such as selective estrogen receptor degraders (SERDs) degrade their receptors through differential recruitment of UBR5 or RNF111. We establish the UBR5 transcriptional regulatory hub as a common mediator and regulator of NR-induced transcription.
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Affiliation(s)
- Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jacob D Aguirre
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Yen-Der Li
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Molecular & Cellular Biology, Harvard University, Cambridge, MA, USA
| | - Jared Brown
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Kater
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Brittany Sandoval
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Stefan Schmitt
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Justine C Rutter
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Pius Galli
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland; Faculty of Science, University of Basel, Basel, Switzerland
| | - Colby R Sandate
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Jevon A Cutler
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Charles Zou
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Ryan J Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Paul M C Park
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Quinlan Sievers
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Charlie Hatton
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Ener
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Brandon D Regalado
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Micah T Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Mikołaj Słabicki
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jeonghyeon Kim
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rebecca Zon
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Zinan Zhang
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Peter G Miller
- Center for Cancer Research, Massachusetts General Hospital, Boston, MA, USA
| | - Roger Belizaire
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA; Division of Pathology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Adam S Sperling
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Rafael Irizarry
- Department of Data Science, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Scott A Armstrong
- Pediatric Hematology-Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| | - Benjamin L Ebert
- Division of Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute, Boston, MA, USA.
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7
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Doamekpor SK, Peng P, Xu R, Ma L, Tong Y, Tong L. A partially open conformation of an androgen receptor ligand-binding domain with drug-resistance mutations. Acta Crystallogr F Struct Biol Commun 2023; 79:95-104. [PMID: 36995121 PMCID: PMC10071832 DOI: 10.1107/s2053230x23002224] [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: 12/27/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
Mutations in the androgen receptor (AR) ligand-binding domain (LBD) can cause resistance to drugs used to treat prostate cancer. Commonly found mutations include L702H, W742C, H875Y, F877L and T878A, while the F877L mutation can convert second-generation antagonists such as enzalutamide and apalutamide into agonists. However, pruxelutamide, another second-generation AR antagonist, has no agonist activity with the F877L and F877L/T878A mutants and instead maintains its inhibitory activity against them. Here, it is shown that the quadruple mutation L702H/H875Y/F877L/T878A increases the soluble expression of AR LBD in complex with pruxelutamide in Escherichia coli. The crystal structure of the quadruple mutant in complex with the agonist dihydrotestosterone (DHT) reveals a partially open conformation of the AR LBD due to conformational changes in the loop connecting helices H11 and H12 (the H11-H12 loop) and Leu881. This partially open conformation creates a larger ligand-binding site for AR. Additional structural studies suggest that both the L702H and F877L mutations are important for conformational changes. This structural variability in the AR LBD could affect ligand binding as well as the resistance to antagonists.
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Affiliation(s)
- Selom K. Doamekpor
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Panfeng Peng
- Suzhou Kintor Pharmaceuticals Inc, No. 20 Songbei Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Ruo Xu
- Suzhou Kintor Pharmaceuticals Inc, No. 20 Songbei Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Liandong Ma
- Suzhou Kintor Pharmaceuticals Inc, No. 20 Songbei Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Youzhi Tong
- Suzhou Kintor Pharmaceuticals Inc, No. 20 Songbei Road, Suzhou Industrial Park, Suzhou, Jiangsu 215123, People’s Republic of China
| | - Liang Tong
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
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8
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Ahmad A, Makhmutova Z, Cao W, Majaz S, Amin A, Xie Y. Androgen receptor, a possible anti-infective therapy target and a potent immune respondent in SARS-CoV-2 spike binding: a computational approach. Expert Rev Anti Infect Ther 2023; 21:317-327. [PMID: 36757420 DOI: 10.1080/14787210.2023.2179035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
BACKGROUND Although androgen in gender disparity of COVID-19 has been implied, no direct link has been provided. RESEARCH DESIGN AND METHODS Here, we applied AlphaFold multimer, network and single cells database analyses to highlight specificity of Androgen receptor (AR) against spike receptor binding protein (RBD) of SARS-CoV-2. RESULTS LXXL motifs in spike RBD are essential for AR binding. RBD LXXA mutation complex with the AR depicting slightly reduced binding energy, as LXXLL motif usually mediates nuclear receptor binding to coregulators. Moreover, AR preferred to bind a LYRL motif in specificity and interaction interface, and showed reduced affinity against Omicron compared to other variants (alpha, beta, gamma, and delta). Importantly, RBD LYRL motif is a conserved antigenic epitope (9 residues) for T-cell response. Network analysis of AR-related genes against COVID-19 database showed T-cell signaling regulation, and CD8+ T-cell spatial location in AR+ single cells, which is consistent with the AR binding motif LYRL in epitope function. CONCLUSIONS We provided the potent mechanisms of AR binding to RBD linking to immune response and vaccination shift. AR could be an anti-infective therapy target for anti-Omicron new lineages.
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Affiliation(s)
- Ashfaq Ahmad
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Zhandaulet Makhmutova
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Wenwen Cao
- Respiratory Department, The Second Affiliated Hospital of Shandong First Medical University, Tai'an, Shandong, China
| | - Sidra Majaz
- Department of Bioinformatics, Hazara University, Mansehra, Pakistan
| | - Amr Amin
- Biology Department, UAE University, Al Ain, UAE
| | - Yingqiu Xie
- Department of Biology, School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
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9
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Ha S, Luo G, Xiang H. A Comprehensive Overview of Small-Molecule Androgen Receptor Degraders: Recent Progress and Future Perspectives. J Med Chem 2022; 65:16128-16154. [PMID: 36459083 DOI: 10.1021/acs.jmedchem.2c01487] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Prostate cancer (PC), the second most prevalent malignancy in men worldwide, has been proven to depend on the aberrant activation of androgen receptor (AR) signaling. Long-term androgen deprivation for the treatment of PC inevitably leads to castration-resistant prostate cancer (CRPC) in which AR remains a crucial oncogenic driver. Thus, there is an urgent need to develop new strategies to address this unmet medical need. Targeting AR for degradation has recently been in a vigorous development stage, and accumulating clinical studies have highlighted the benefits of AR degraders in CRPC patients. Herein, we provide a comprehensive summary of small-molecule AR degraders with diverse mechanisms of action including proteolysis-targeting chimeras (PROTACs), selective AR degraders (SARDs), hydrophobic tags (HyT), and other AR degraders with distinct mechanisms. Accordingly, their structure-activity relationships, biomedical applications, and therapeutic values are also dissected to provide insights into the future development of promising AR degradation-based therapeutics for CRPC.
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Affiliation(s)
- Si Ha
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
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10
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Zhang F, Biswas M, Massah S, Lee J, Lingadahalli S, Wong S, Wells C, Foo J, Khan N, Morin H, Saxena N, Kung SY, Sun B, Parra Nuñez A, Sanchez C, Chan N, Ung L, Altıntaş U, Bui J, Wang Y, Fazli L, Oo H, Rennie P, Lack N, Cherkasov A, Gleave M, Gsponer J, Lallous N. Dynamic phase separation of the androgen receptor and its coactivators key to regulate gene expression. Nucleic Acids Res 2022; 51:99-116. [PMID: 36535377 PMCID: PMC9841400 DOI: 10.1093/nar/gkac1158] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 10/27/2022] [Accepted: 11/21/2022] [Indexed: 12/24/2022] Open
Abstract
Numerous cancers, including prostate cancer (PCa), are addicted to transcription programs driven by specific genomic regions known as super-enhancers (SEs). The robust transcription of genes at such SEs is enabled by the formation of phase-separated condensates by transcription factors and coactivators with intrinsically disordered regions. The androgen receptor (AR), the main oncogenic driver in PCa, contains large disordered regions and is co-recruited with the transcriptional coactivator mediator complex subunit 1 (MED1) to SEs in androgen-dependent PCa cells, thereby promoting oncogenic transcriptional programs. In this work, we reveal that full-length AR forms foci with liquid-like properties in different PCa models. We demonstrate that foci formation correlates with AR transcriptional activity, as this activity can be modulated by changing cellular foci content chemically or by silencing MED1. AR ability to phase separate was also validated in vitro by using recombinant full-length AR protein. We also demonstrate that AR antagonists, which suppress transcriptional activity by targeting key regions for homotypic or heterotypic interactions of this receptor, hinder foci formation in PCa cells and phase separation in vitro. Our results suggest that enhanced compartmentalization of AR and coactivators may play an important role in the activation of oncogenic transcription programs in androgen-dependent PCa.
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Affiliation(s)
- Fan Zhang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | | | | | - Joseph Lee
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Shreyas Lingadahalli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Samantha Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Christopher Wells
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Jane Foo
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Nabeel Khan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Helene Morin
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Neetu Saxena
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Sonia H Y Kung
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Bei Sun
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Ana Karla Parra Nuñez
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Christophe Sanchez
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Novia Chan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Lauren Ung
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Umut Berkay Altıntaş
- School of Medicine, Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey
| | - Jennifer M Bui
- Michael Smith Laboratories, Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Htoo Zarni Oo
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Paul S Rennie
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada,School of Medicine, Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey,Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Rumelifeneri Yolu, Istanbul 34450, Turkey
| | - Artem Cherkasov
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, 2660 Oak St., Vancouver, BC V6H 3Z6, Canada
| | - Jörg Gsponer
- Correspondence may also be addressed to Jörg Gsponer.
| | - Nada Lallous
- To whom correspondence should be addressed. Tel: +1 604 875 4111; Fax: +1 604 875 5654;
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11
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Abstract
Efforts to decrease the adverse effects of nuclear receptor (NR) drugs have yielded experimental agonists that produce better outcomes in mice. Some of these agonists have been shown to cause different, not just less intense, on-target transcriptomic effects; however, a structural explanation for such agonist-specific effects remains unknown. Here, we show that partial agonists of the NR peroxisome proliferator-associated receptor γ (PPARγ), which induce better outcomes in mice compared to clinically utilized type II diabetes PPARγ-binding drugs thiazolidinediones (TZDs), also favor a different group of coactivator peptides than the TZDs. We find that PPARγ full agonists can also be biased relative to each other in terms of coactivator peptide binding. We find differences in coactivator-PPARγ bonding between the coactivator subgroups which allow agonists to favor one group of coactivator peptides over another, including differential bonding to a C-terminal residue of helix 4. Analysis of all available NR-coactivator structures indicates that such differential helix 4 bonding persists across other NR-coactivator complexes, providing a general structural mechanism of biased agonism for many NRs. Further work will be necessary to determine if such bias translates into altered coactivator occupancy and physiology in cells.
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12
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Wang Q, Wang Z, Tian S, Wang L, Tang R, Yu Y, Ge J, Hou T, Hao H, Sun H. Determination of Molecule Category of Ligands Targeting the Ligand-Binding Pocket of Nuclear Receptors with Structural Elucidation and Machine Learning. J Chem Inf Model 2022; 62:3993-4007. [PMID: 36040137 DOI: 10.1021/acs.jcim.2c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of transcriptional activation/repression of the nuclear receptors (NRs) involves two main conformations of the NR protein, namely, the active (agonistic) and inactive (antagonistic) conformations. Binding of agonists or antagonists to the ligand-binding pocket (LBP) of NRs can regulate the downstream signaling pathways with different physiological effects. However, it is still hard to determine the molecular type of a LBP-bound ligand because both the agonists and antagonists bind to the same position of the protein. Therefore, it is necessary to develop precise and efficient methods to facilitate the discrimination of agonists and antagonists targeting the LBP of NRs. Here, combining structural and energetic analyses with machine-learning (ML) algorithms, we constructed a series of structure-based ML models to determine the molecular category of the LBP-bound ligands. We show that the proposed models work robustly and with high accuracy (ACC > 0.9) for determining the category of molecules derived from docking-based and crystallized poses. Furthermore, the models are also capable of determining the molecular category of ligands with dual opposite functions on different NRs (i.e., working as an agonist in one NR target, whereas functioning as an antagonist in another) with reasonable accuracy. The proposed method is expected to facilitate the determination of the molecular properties of ligands targeting the LBP of NRs with structural interpretation.
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Affiliation(s)
- Qinghua Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Zhe Wang
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Sheng Tian
- Department of Medicinal Chemistry, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, P. R. China
| | - Lingling Wang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Rongfan Tang
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Yang Yu
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
| | - Jingxuan Ge
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China.,Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Tingjun Hou
- Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, Zhejiang, P. R. China
| | - Haiping Hao
- State Key Laboratory of Natural Medicines, Key Lab of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, 210009 Nanjing, China
| | - Huiyong Sun
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, Jiangsu, P. R. China
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13
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Mobisson SK, Ikpi DE, Wopara I, Obembe AO, Omotuyi O. Inhibition of human androgen receptor by delta 9-tetrahydro-cannabinol and cannabidiol related to reproductive dysfunction: A computational study. Andrologia 2022; 54:e14454. [PMID: 35524041 DOI: 10.1111/and.14454] [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: 03/11/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 12/01/2022] Open
Abstract
There have been conflicting reports on the impact of Cannabis sativa impact on reproductive function. Hence this study was aimed to ascertain the impact of tetrahydrocannabinol (THC) and cannabidiol (CBD) binding affinity on human androgen receptor (AR) via computational molecular dynamic simulation. The human AR coordinate in this study is derived from human AR in complex with the ligand metribolone (R18) (PBD ID: 1E3G) template using (MODELER version. 9.15). CBD (PubChem CID: 644019), and THC (PubChem CID: 16078) 2D structures were retrieved from PubChem and docked (Autodock-Vina inbuilt in PyMol into the active site of human AR using the coordinates of the co-crystalized ligand (R18). All atomic representations in this study were created using visual molecular dynamics (VMD) tools. The result revealed that neither CBD nor THC bear significant 2D similarity with R18. Despite the diversity within the chemical space, both CBD and THC poses bond flexibility required to bind avidly to AR with the docking scores comparable to R18. In fully bound state, the three compounds engage the AR pocket hydrophobic residues such as L701, L704, and L707, and aromatic residues such as F764. Polar contacts with T877 observed in R18 bound state is avoided in the THC and CBD bound states. Moreso, the results revealed that CBD has lesser binding energy compared to THC and R18 compound which serves as standard. This study hypothesized that CBD and THC binds complimentarily to the pocket AR, indicating a likely inhibition of reproductive function and prostate cancer progression.
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Affiliation(s)
- Samuel Kelechi Mobisson
- Department of Human Physiology, Faculty of Basic Medical Sciences, Madonna University, Elele, Rivers State, Nigeria
| | - Daniel Ewa Ikpi
- Department of Human Physiology, Faculty of Basic Medical Sciences, University of Calabar, Calabar, Cross River State, Nigeria
| | - Iheanyichukwu Wopara
- Department of Biochemistry, Faculty of Sciences, University of Port Harcourt, Port Harcourt, Rivers State, Nigeria
| | - Agona Odey Obembe
- Department of Human Physiology, Faculty of Basic Medical Sciences, University of Calabar, Calabar, Cross River State, Nigeria
| | - Olaposi Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado Ekiti, Nigeria
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14
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Han Z, Xue J, Li Y. Phthalate's multiple hormonal effects and their supplementary dietary regulation scheme of health risks for children. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:29016-29032. [PMID: 34993781 DOI: 10.1007/s11356-021-17798-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Four common phthalic acid esters (PAEs), namely, butylbenzyl phthalate (BBzP), dibutyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP), and di-n-octyl phthalate (DNOP) that are known to affect children upon exposure, were selected, and the hormone effects were explored during different supplementary food intakes by using methods such as factorial design experiment, molecular docking, and dynamics simulation techniques. A supplementary diet regulation scheme to prevent health risks of PAEs was constructed to avoid or mitigate the hormonal effects in children exposed to PAEs. Firstly, the MM/PBSA binding energy of PAEs with single hormone receptors and multiple hormone receptor complexes was calculated. In addition, 10 foods were selected as external interference conditions to carry out dynamic simulation, which showed that kiwi fruit and broccoli can effectively alleviate the PAEs' hormone effects. Furthermore, inference of the metabolic process of DEHP found that the supplementary diets could effectively promote the metabolism of PAEs. Finally, based on the mechanism analysis, it was confirmed that the selected supplementary diets could inhibit the binding process. This study aims to explore the role of supplementary diets in regulating various PAEs' hormone effects and thereby provide theoretical support for slowing down hormonal effects in children.
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Affiliation(s)
- Zhenzhen Han
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Jiaqi Xue
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yu Li
- Key Laboratory of Resource and Environmental System Optimization, Ministry of Education, North China Electric Power University, Beijing, 102206, China.
- College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
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15
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Dahiya UR, Heemers HV. Analyzing the Androgen Receptor Interactome in Prostate Cancer: Implications for Therapeutic Intervention. Cells 2022; 11:cells11060936. [PMID: 35326387 PMCID: PMC8946651 DOI: 10.3390/cells11060936] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
The androgen receptor (AR) is a member of the ligand-activated nuclear receptor family of transcription factors. AR’s transactivation activity is turned on by the binding of androgens, the male sex steroid hormones. AR is critical for the development and maintenance of the male phenotype but has been recognized to also play an important role in human diseases. Most notably, AR is a major driver of prostate cancer (CaP) progression, which remains the second leading cause of cancer deaths in American men. Androgen deprivation therapies (ADTs) that interfere with interactions between AR and its activating androgen ligands have been the mainstay for treatment of metastatic CaP. Although ADTs are effective and induce remissions, eventually they fail, while the growth of the majority of ADT-resistant CaPs remains under AR’s control. Alternative approaches to inhibit AR activity and bypass resistance to ADT are being sought, such as preventing the interaction between AR and its cofactors and coregulators that is needed to execute AR-dependent transcription. For such strategies to be efficient, the 3D conformation of AR complexes needs to be well-understood and AR-regulator interaction sites resolved. Here, we review current insights into these 3D structures and the protein interaction sites in AR transcriptional complexes. We focus on methods and technological approaches used to identify AR interactors and discuss challenges and limitations that need to be overcome for efficient therapeutic AR complex disruption.
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16
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Gentile F, Yaacoub JC, Gleave J, Fernandez M, Ton AT, Ban F, Stern A, Cherkasov A. Artificial intelligence-enabled virtual screening of ultra-large chemical libraries with deep docking. Nat Protoc 2022; 17:672-697. [PMID: 35121854 DOI: 10.1038/s41596-021-00659-2] [Citation(s) in RCA: 96] [Impact Index Per Article: 48.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 11/08/2021] [Indexed: 12/14/2022]
Abstract
With the recent explosion of chemical libraries beyond a billion molecules, more efficient virtual screening approaches are needed. The Deep Docking (DD) platform enables up to 100-fold acceleration of structure-based virtual screening by docking only a subset of a chemical library, iteratively synchronized with a ligand-based prediction of the remaining docking scores. This method results in hundreds- to thousands-fold virtual hit enrichment (without significant loss of potential drug candidates) and hence enables the screening of billion molecule-sized chemical libraries without using extraordinary computational resources. Herein, we present and discuss the generalized DD protocol that has been proven successful in various computer-aided drug discovery (CADD) campaigns and can be applied in conjunction with any conventional docking program. The protocol encompasses eight consecutive stages: molecular library preparation, receptor preparation, random sampling of a library, ligand preparation, molecular docking, model training, model inference and the residual docking. The standard DD workflow enables iterative application of stages 3-7 with continuous augmentation of the training set, and the number of such iterations can be adjusted by the user. A predefined recall value allows for control of the percentage of top-scoring molecules that are retained by DD and can be adjusted to control the library size reduction. The procedure takes 1-2 weeks (depending on the available resources) and can be completely automated on computing clusters managed by job schedulers. This open-source protocol, at https://github.com/jamesgleave/DD_protocol , can be readily deployed by CADD researchers and can significantly accelerate the effective exploration of ultra-large portions of a chemical space.
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Affiliation(s)
- Francesco Gentile
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Jean Charle Yaacoub
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - James Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Michael Fernandez
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Anh-Tien Ton
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | - Fuqiang Ban
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada
| | | | - Artem Cherkasov
- Vancouver Prostate Centre, Department of Urologic Sciences, The University of British Columbia, Vancouver, BC, Canada.
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17
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Samchenko AA, Komarov VM, Kondratyev MS. The Study of Steroid Keys for Androgen Receptors. Biophysics (Nagoya-shi) 2021. [DOI: 10.1134/s0006350921050213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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18
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Özgün F, Kaya Z, Morova T, Geverts B, Abraham TE, Houtsmuller AB, van Royen ME, Lack NA. DNA binding alters ARv7 dimer interactions. J Cell Sci 2021; 134:jcs258332. [PMID: 34318896 DOI: 10.1242/jcs.258332] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/02/2021] [Indexed: 11/20/2022] Open
Abstract
Androgen receptor (AR) splice variants are proposed to be a potential driver of lethal castration-resistant prostate cancer. AR splice variant 7 (ARv7) is the most commonly observed isoform and strongly correlates with resistance to second-generation anti-androgens. Despite this clinical evidence, the interplay between ARv7 and the highly expressed full-length AR (ARfl) remains unclear. In this work, we show that ARfl/ARv7 heterodimers readily form in the nucleus via an intermolecular N/C interaction that brings the four termini of the proteins in close proximity. Combining fluorescence resonance energy transfer and fluorescence recovery after photobleaching, we demonstrate that these heterodimers undergo conformational changes following DNA binding, indicating dynamic nuclear receptor interaction. Although transcriptionally active, ARv7 can only form short-term interactions with DNA at highly accessible high-occupancy ARfl binding sites. Dimerization with ARfl does not affect ARv7 binding dynamics, suggesting that DNA binding occupancy is determined by the individual protein monomers and not the homodimer or heterodimer complex. Overall, these biophysical studies reveal detailed properties of ARv7 dynamics as both a homodimer or heterodimer with ARfl.
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Affiliation(s)
- Fatma Özgün
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Zeynep Kaya
- School of Medicine, Koç University, Istanbul 34450, Turkey
| | - Tunç Morova
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
| | - Bart Geverts
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Tsion E Abraham
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Adriaan B Houtsmuller
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Martin E van Royen
- Erasmus Optical Imaging Centre, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
- Department of Pathology, Erasmus University Medical Center, 3015 GE Rotterdam, The Netherlands
| | - Nathan A Lack
- School of Medicine, Koç University, Istanbul 34450, Turkey
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC V6H 3Z6, Canada
- Koç University Research Centre for Translational Medicine (KUTTAM), Koç University, Istanbul 34450, Turkey
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19
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Kong X, Xing E, Zhuang T, Li PK, Cheng X. Mechanistic Insights into the Allosteric Inhibition of Androgen Receptors by Binding Function 3 Antagonists from an Integrated Molecular Modeling Study. J Chem Inf Model 2021; 61:3477-3494. [PMID: 34165949 DOI: 10.1021/acs.jcim.1c00124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An androgen receptor (AR) is an intensively studied treatment target for castration-resistant prostate cancer that is irresponsive to conventional antiandrogen therapeutics. Binding function 3 (BF3) inhibitors with alternative modes of action have emerged as a promising approach to overcoming antiandrogen resistance. However, how these BF3 inhibitors modulate AR function remains elusive, hindering the development of BF3-targeting agents. Here, we performed an integrated computational study to interrogate the binding mechanism of several known BF3 inhibitors with ARs. Our results show that the inhibitory effect of the BF3 antagonists arises from their allosteric modulation of the activation function (AF2) site, which alters the dynamic coupling between the BF3 and AF2 sites as well as the AF2-coactivator (SRC2-3) interaction. Moreover, the per-residue binding energy analyses reveal the "anchor" role of the linker connecting the phenyl ring and benzimidazole/indole in these BF3 inhibitors. Furthermore, the allosteric driver-interacting residues are found to include both "positive", e.g., Phe673 and Asn833, and "negative" ones, e.g., Phe826, and the differential interactions with these residues provide an explanation why stronger binding does not necessarily result in higher inhibitory activities. Finally, our allosteric communication pathway analyses delineate how the allosteric signals triggered by BF3 binding are propagated to the AF2 pocket through multiple short- and/or long-ranged transmission pathways. Collectively, our combined computational study provides a comprehensive structural mechanism underlying how the selected set of BF3 inhibitors modulate AR function, which will help guide future development of BF3 antagonists.
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Affiliation(s)
- Xiaotian Kong
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Enming Xing
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Tony Zhuang
- J. Willis Hurst Internal Medicine Program, Department of Medicine, Emory University, 100 Woodruff Circle, Atlanta, Georgia 30329, United States
| | - Pui-Kai Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio 43210, United States
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20
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Structural Insights into the Interaction of the Intrinsically Disordered Co-activator TIF2 with Retinoic Acid Receptor Heterodimer (RXR/RAR). J Mol Biol 2021; 433:166899. [PMID: 33647291 DOI: 10.1016/j.jmb.2021.166899] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/02/2021] [Accepted: 02/22/2021] [Indexed: 12/19/2022]
Abstract
Retinoic acid receptors (RARs) and retinoid X receptors (RXRs) form heterodimers that activate target gene transcription by recruiting co-activator complexes in response to ligand binding. The nuclear receptor (NR) co-activator TIF2 mediates this recruitment by interacting with the ligand-binding domain (LBD) of NRs trough the nuclear receptor interaction domain (TIF2NRID) containing three highly conserved α-helical LxxLL motifs (NR-boxes). The precise binding mode of this domain to RXR/RAR is not clear due to the disordered nature of TIF2. Here we present the structural characterization of TIF2NRID by integrating several experimental (NMR, SAXS, Far-UV CD, SEC-MALS) and computational data. Collectively, the data are in agreement with a largely disordered protein with partially structured regions, including the NR-boxes and their flanking regions, which are evolutionary conserved. NMR and X-ray crystallographic data on TIF2NRID in complex with RXR/RAR reveal a multisite binding of the three NR-boxes as well as an active role of their flanking regions in the interaction.
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21
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Phasing the intranuclear organization of steroid hormone receptors. Biochem J 2021; 478:443-461. [DOI: 10.1042/bcj20200883] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/28/2020] [Accepted: 01/07/2021] [Indexed: 12/15/2022]
Abstract
Steroid receptors (SRs) encompass a family of transcription factors that regulate the expression of thousands of genes upon binding to steroid hormones and include the glucocorticoid, androgen, progesterone, estrogen and mineralocorticoid receptors. SRs control key physiological and pathological processes, thus becoming relevant drug targets. As with many other nuclear proteins, hormone-activated SRs concentrate in multiple discrete foci within the cell nucleus. Even though these foci were first observed ∼25 years ago, their exact structure and function remained elusive. In the last years, new imaging methodologies and theoretical frameworks improved our understanding of the intranuclear organization. These studies led to a new paradigm stating that many membraneless nuclear compartments, including transcription-related foci, form through a liquid–liquid phase separation process. These exciting ideas impacted the SR field by raising the hypothesis of SR foci as liquid condensates involved in transcriptional regulation. In this work, we review the current knowledge about SR foci formation under the light of the condensate model, analyzing how these structures may impact SR function. These new ideas, combined with state-of-the-art techniques, may shed light on the biophysical mechanisms governing the formation of SR foci and the biological function of these structures in normal physiology and disease.
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22
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Asangani I, Blair IA, Van Duyne G, Hilser VJ, Moiseenkova-Bell V, Plymate S, Sprenger C, Wand AJ, Penning TM. Using biochemistry and biophysics to extinguish androgen receptor signaling in prostate cancer. J Biol Chem 2021; 296:100240. [PMID: 33384381 PMCID: PMC7949100 DOI: 10.1074/jbc.rev120.012411] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 12/19/2020] [Accepted: 12/31/2020] [Indexed: 12/12/2022] Open
Abstract
Castration resistant prostate cancer (CRPC) continues to be androgen receptor (AR) driven. Inhibition of AR signaling in CRPC could be advanced using state-of-the-art biophysical and biochemical techniques. Structural characterization of AR and its complexes by cryo-electron microscopy would advance the development of N-terminal domain (NTD) and ligand-binding domain (LBD) antagonists. The structural basis of AR function is unlikely to be determined by any single structure due to the intrinsic disorder of its NTD, which not only interacts with coregulators but likely accounts for the constitutive activity of AR-splice variants (SV), which lack the LBD and emerge in CRPC. Using different AR constructs lacking the LBD, their effects on protein folding, DNA binding, and transcriptional activity could reveal how interdomain coupling explains the activity of AR-SVs. The AR also interacts with coregulators that promote chromatin looping. Elucidating the mechanisms involved can identify vulnerabilities to treat CRPC, which do not involve targeting the AR. Phosphorylation of the AR coactivator MED-1 by CDK7 is one mechanism that can be blocked by the use of CDK7 inhibitors. CRPC gains resistance to AR signaling inhibitors (ARSI). Drug resistance may involve AR-SVs, but their role requires their reliable quantification by SILAC-mass spectrometry during disease progression. ARSI drug resistance also occurs by intratumoral androgen biosynthesis catalyzed by AKR1C3 (type 5 17β-hydroxysteroid dehydrogenase), which is unique in that its acts as a coactivator of AR. Novel bifunctional inhibitors that competitively inhibit AKR1C3 and block its coactivator function could be developed using reverse-micelle NMR and fragment-based drug discovery.
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Affiliation(s)
- Irfan Asangani
- Department Cancer Biology, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ian A Blair
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Gregory Van Duyne
- Department of Biochemistry & Biophysics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vera Moiseenkova-Bell
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Stephen Plymate
- Division of Gerontology & Geriatric Medicine, Department of Medicine, University of Washington, and GRECC, Seattle, Washington, USA
| | - Cynthia Sprenger
- Division of Gerontology & Geriatric Medicine, Department of Medicine, University of Washington, and GRECC, Seattle, Washington, USA
| | - A Joshua Wand
- Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas, USA
| | - Trevor M Penning
- Department Systems Pharmacology & Translational Therapeutics, Perelman School of Medicine University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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23
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Yu X, Yi P, Hamilton RA, Shen H, Chen M, Foulds CE, Mancini MA, Ludtke SJ, Wang Z, O'Malley BW. Structural Insights of Transcriptionally Active, Full-Length Androgen Receptor Coactivator Complexes. Mol Cell 2020; 79:812-823.e4. [PMID: 32668201 DOI: 10.1016/j.molcel.2020.06.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 01/15/2023]
Abstract
Steroid receptors activate gene transcription by recruiting coactivators to initiate transcription of their target genes. For most nuclear receptors, the ligand-dependent activation function domain-2 (AF-2) is a primary contributor to the nuclear receptor (NR) transcriptional activity. In contrast to other steroid receptors, such as ERα, the activation function of androgen receptor (AR) is largely dependent on its ligand-independent AF-1 located in its N-terminal domain (NTD). It remains unclear why AR utilizes a different AF domain from other receptors despite that NRs share similar domain organizations. Here, we present cryoelectron microscopy (cryo-EM) structures of DNA-bound full-length AR and its complex structure with key coactivators, SRC-3 and p300. AR dimerization follows a unique head-to-head and tail-to-tail manner. Unlike ERα, AR directly contacts a single SRC-3 and p300. The AR NTD is the primary site for coactivator recruitment. The structures provide a basis for understanding assembly of the AR:coactivator complex and its domain contributions for coactivator assembly and transcriptional regulation.
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Affiliation(s)
- Xinzhe Yu
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ping Yi
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ross A Hamilton
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Hong Shen
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muyuan Chen
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Charles E Foulds
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Michael A Mancini
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Steven J Ludtke
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Zhao Wang
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Bert W O'Malley
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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24
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Gentile F, Agrawal V, Hsing M, Ton AT, Ban F, Norinder U, Gleave ME, Cherkasov A. Deep Docking: A Deep Learning Platform for Augmentation of Structure Based Drug Discovery. ACS CENTRAL SCIENCE 2020; 6:939-949. [PMID: 32607441 PMCID: PMC7318080 DOI: 10.1021/acscentsci.0c00229] [Citation(s) in RCA: 149] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Indexed: 05/06/2023]
Abstract
Drug discovery is a rigorous process that requires billion dollars of investments and decades of research to bring a molecule "from bench to a bedside". While virtual docking can significantly accelerate the process of drug discovery, it ultimately lags the current rate of expansion of chemical databases that already exceed billions of molecular records. This recent surge of small molecules availability presents great drug discovery opportunities, but also demands much faster screening protocols. In order to address this challenge, we herein introduce Deep Docking (DD), a novel deep learning platform that is suitable for docking billions of molecular structures in a rapid, yet accurate fashion. The DD approach utilizes quantitative structure-activity relationship (QSAR) deep models trained on docking scores of subsets of a chemical library to approximate the docking outcome for yet unprocessed entries and, therefore, to remove unfavorable molecules in an iterative manner. The use of DD methodology in conjunction with the FRED docking program allowed rapid and accurate calculation of docking scores for 1.36 billion molecules from the ZINC15 library against 12 prominent target proteins and demonstrated up to 100-fold data reduction and 6000-fold enrichment of high scoring molecules (without notable loss of favorably docked entities). The DD protocol can readily be used in conjunction with any docking program and was made publicly available.
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Affiliation(s)
- Francesco Gentile
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Vibudh Agrawal
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Michael Hsing
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Anh-Tien Ton
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Fuqiang Ban
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Ulf Norinder
- Swetox,
Unit of Toxicology Sciences, Karolinska
Institutet, Forskargatan
20, SE-151 36 Södertalje, Sweden
- Department
of Computer and Systems Sciences, Stockholm
University, Box 7003, SE-164
07 Kista, Sweden
| | - Martin E. Gleave
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
| | - Artem Cherkasov
- Vancouver
Prostate Centre, University of British Columbia, Vancouver, British Columbia V6H3Z6, Canada
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25
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Takahashi M, Ubukata O, Homma T, Asoh Y, Honzumi M, Hayashi N, Saito K, Tsuruoka H, Aoki K, Hanzawa H. Crystal structure of the mineralocorticoid receptor ligand-binding domain in complex with a potent and selective nonsteroidal blocker, esaxerenone (CS-3150). FEBS Lett 2020; 594:1615-1623. [PMID: 31991486 DOI: 10.1002/1873-3468.13746] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/08/2020] [Accepted: 01/15/2020] [Indexed: 12/24/2022]
Abstract
Activation of the mineralocorticoid receptor (MR) has long been considered a risk factor for cardiovascular diseases. It has been reported that the novel MR blocker esaxerenone shows high potency and selectivity for MR in vitro as well as great antihypertensive and renoprotective effects in salt-sensitive hypertensive rats. Here, we determined the cocrystal structure of the MR ligand-binding domain (MR-LBD) with esaxerenone and found that esaxerenone binds to MR-LBD in a unique manner with large side-chain rearrangements, distinct from those of previously published MR antagonists. This structure also displays an antagonist form that has not been observed for MR previously. Such a unique binding mode of esaxerenone provides great insight into the novelty, potency, and selectivity of this novel antihypertensive drug.
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Affiliation(s)
- Mizuki Takahashi
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd., Tokyo, Japan
| | - Osamu Ubukata
- Protein Production Research Group, Biological Research Department, Daiichi Sankyo RD Novare Co., Ltd., Tokyo, Japan
| | - Tsuyoshi Homma
- Global Project Management Department, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Yusuke Asoh
- IT Strategy Department, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Masatoshi Honzumi
- Process Technology Research Laboratories, Daiichi Sankyo Co., Ltd., Kanagawa, Japan
| | - Noriyuki Hayashi
- Medicinal Chemistry Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Keiji Saito
- Medicinal Chemistry Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Hiroyuki Tsuruoka
- Intellectual property department, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Kazumasa Aoki
- Medicinal Chemistry Research Laboratories, Daiichi Sankyo Co., Ltd., Tokyo, Japan
| | - Hiroyuki Hanzawa
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd., Tokyo, Japan
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26
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Selvaraj D, Muthu S, Kotha S, Siddamsetty RS, Andavar S, Jayaraman S. Syringaresinol as a novel androgen receptor antagonist against wild and mutant androgen receptors for the treatment of castration-resistant prostate cancer: molecular docking, in-vitro and molecular dynamics study. J Biomol Struct Dyn 2020; 39:621-634. [PMID: 31928160 DOI: 10.1080/07391102.2020.1715261] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phytoestrogens are dietary estrogens having similar structure as of estrogen. Some of these phytoestrogens are androgen receptor (AR) antagonists and exhibit preventive role in the prostate cancer. However, in androgen-independent prostate cancer (AIPC) the ARs were mutated (T877A, W741L, F876L, etc.) and these mutant ARs convert the antagonist to agonist. Our aim in this study is to find phytoestrogens that could function as an antagonist with wild and mutant ARs. The phytoestrogens were analyzed for binding affinity with wild and mutant ARs in agonist and antagonist conformations. The point mutations were carried out using Chimera. The antagonist AR conformation was modeled using Modeller. We hypothesize that the compounds having binding affinity with agonist AR conformation could not function as a full or pure antagonist. Most of the phytoestrogens have binding affinity with agonist AR conformation contradicting previous results. For example, genistein which is a widely studied isoflavone has known AR antagonist property. However, in our study, it had good binding affinity with agonist AR conformation. Hence, to confirm our hypothesis, we tested genistein in LNCaP (T877A mutant AR) cells by qPCR studies. The genistein functioned as an antagonist only in the presence of an androgen indicting a partial agonist type of activity. The in-vitro results supported our docking hypothesis. We applied this principle and found syringaresinol could function as an antagonist with wild and mutated ARs. Further, we carried out molecular dynamics for the hit molecule to confirm its antagonist binding mode with mutant AR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Divakar Selvaraj
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
| | - Santhoshkumar Muthu
- Department of Biotechnology, Rathinam College of Arts and Science, Coimbatore, Tamilnadu, India
| | - Satvik Kotha
- Department of Pharmacology, Government College of Pharmacy, Bengaluru, Karnataka, India
| | | | - Sasikumar Andavar
- Department of Chemistry, Anthem Biosciences Pvt. Ltd., Bengaluru, Karnataka, India
| | - Saravanan Jayaraman
- Department of Pharmacology, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Ooty, Tamilnadu, India
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27
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Fancher AT, Hua Y, Strock CJ, Johnston PA. Assays to Interrogate the Ability of Compounds to Inhibit the AF-2 or AF-1 Transactivation Domains of the Androgen Receptor. Assay Drug Dev Technol 2019; 17:364-386. [PMID: 31502857 DOI: 10.1089/adt.2019.940] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Prostate cancer is the leading cause of cancer and second leading cause of cancer-related death in men in the United States. Twenty percent of patients receiving the standard of care androgen deprivation therapy (ADT) eventually progress to metastatic and incurable castration-resistant prostate cancer (CRPC). Current FDA-approved drugs for CRPC target androgen receptor (AR) binding or androgen production, but only provide a 2- to 5-month survival benefit due to the emergence of resistance. Overexpression of AR coactivators and the emergence of AR splice variants, both promote continued transcriptional activation under androgen-depleted conditions and represent drug resistance mechanisms that contribute to CRPC progression. The AR contains two transactivation domains, activation function 2 (AF-2) and activation function 1 (AF-1), which serve as binding surfaces for coactivators involved in the transcriptional activation of AR target genes. Full-length AR contains both AF-2 and AF-1 surfaces, whereas AR splice variants only have an AF-1 surface. We have recently prosecuted a high-content screening campaign to identify hit compounds that can inhibit or disrupt the protein-protein interactions (PPIs) between AR and transcriptional intermediary factor 2 (TIF2), one of the coactivators implicated in CRPC disease progression. Since an ideal inhibitor/disruptor of AR-coactivator PPIs would target both the AF-2 and AF-1 surfaces, we describe here the development and validation of five AF-2- and three AF-1-focused assays to interrogate and prioritize hits that disrupt both transactivation surfaces. The assays were validated using a test set of seven known AR modulator compounds, including three AR antagonists and one androgen synthesis inhibitor that are FDA-approved ADTs, two investigational molecules that target the N-terminal domain of AR, and an inhibitor of the Hsp90 (heat shock protein) molecular chaperone.
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Affiliation(s)
- Ashley T Fancher
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yun Hua
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania
| | | | - Paul A Johnston
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Pittsburgh, Pittsburgh, Pennsylvania.,Head and Neck Cancer, and Skin Cancer Specialized Programs of Research Excellence, University of Pittsburgh Hillman Cancer Center, Pittsburgh, Pennsylvania
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28
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Skowron KJ, Booker K, Cheng C, Creed S, David BP, Lazzara PR, Lian A, Siddiqui Z, Speltz TE, Moore TW. Steroid receptor/coactivator binding inhibitors: An update. Mol Cell Endocrinol 2019; 493:110471. [PMID: 31163202 PMCID: PMC6645384 DOI: 10.1016/j.mce.2019.110471] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/30/2019] [Accepted: 05/30/2019] [Indexed: 12/14/2022]
Abstract
The purpose of this review is to highlight recent developments in small molecules and peptides that block the binding of coactivators to steroid receptors. These coactivator binding inhibitors bind at the coregulator binding groove, also known as Activation Function-2, rather than at the ligand-binding site of steroid receptors. Steroid receptors that have been targeted with coactivator binding inhibitors include the androgen receptor, estrogen receptor and progesterone receptor. Coactivator binding inhibitors may be useful in some cases of resistance to currently prescribed therapeutics. The scope of the review includes small-molecule and peptide coactivator binding inhibitors for steroid receptors, with a particular focus on recent compounds that have been assayed in cell-based models.
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Affiliation(s)
- Kornelia J Skowron
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Kenneth Booker
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Changfeng Cheng
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Simone Creed
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Brian P David
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Phillip R Lazzara
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Amy Lian
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Zamia Siddiqui
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA
| | - Thomas E Speltz
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; Department of Chemistry, University of Chicago, 929 E. 57th Street, E547, Chicago, IL, 60637, USA
| | - Terry W Moore
- Department of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, University of Illinois at Chicago, 833 S. Wood Street, Chicago, IL, 60612, USA; University of Illinois Cancer Center, University of Illinois at Chicago, 1801 W. Taylor Street, Chicago, IL, 60612, USA.
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29
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Woo ARE, Sze SK, Chung HH, Lin VCL. Delineation of critical amino acids in activation function 1 of progesterone receptor for recruitment of transcription coregulators. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:522-533. [DOI: 10.1016/j.bbagrm.2019.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 01/30/2019] [Indexed: 12/17/2022]
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30
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Monczor F, Chatzopoulou A, Zappia CD, Houtman R, Meijer OC, Fitzsimons CP. A Model of Glucocorticoid Receptor Interaction With Coregulators Predicts Transcriptional Regulation of Target Genes. Front Pharmacol 2019; 10:214. [PMID: 30930776 PMCID: PMC6425864 DOI: 10.3389/fphar.2019.00214] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/20/2019] [Indexed: 12/14/2022] Open
Abstract
Regulatory factors that control gene transcription in multicellular organisms are assembled in multicomponent complexes by combinatorial interactions. In this context, nuclear receptors provide well-characterized and physiologically relevant systems to study ligand-induced transcription resulting from the integration of cellular and genomic information in a cell- and gene-specific manner. Here, we developed a mathematical model describing the interactions between the glucocorticoid receptor (GR) and other components of a multifactorial regulatory complex controlling the transcription of GR-target genes, such as coregulator peptides. We support the validity of the model in relation to gene-specific GR transactivation with gene transcription data from A549 cells and in vitro real time quantification of coregulator-GR interactions. The model accurately describes and helps to interpret ligand-specific and gene-specific transcriptional regulation by the GR. The comprehensive character of the model allows future insight into the function and relative contribution of the molecular species proposed in ligand- and gene-specific transcriptional regulation.
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Affiliation(s)
- Federico Monczor
- Laboratorio de Farmacología de Receptores, Instituto de Investigaciones Farmacológicas, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - Antonia Chatzopoulou
- Leiden Academic Center for Drug Research, Leiden University, Leiden, Netherlands
| | - Carlos Daniel Zappia
- Laboratorio de Farmacología de Receptores, Instituto de Investigaciones Farmacológicas, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina
| | - René Houtman
- PamGene International B.V., 's-Hertogenbosch, Netherlands
| | - Onno C Meijer
- Division of Endocrinology, Department of Internal Medicine, Leiden University Medical Centre, Leiden, Netherlands
| | - Carlos P Fitzsimons
- Neuroscience Collaboration, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
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31
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Moretto L, Heylen R, Holroyd N, Vance S, Broadhurst RW. Modular type I polyketide synthase acyl carrier protein domains share a common N-terminally extended fold. Sci Rep 2019; 9:2325. [PMID: 30787330 PMCID: PMC6382882 DOI: 10.1038/s41598-019-38747-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 11/15/2018] [Indexed: 11/09/2022] Open
Abstract
Acyl carrier protein (ACP) domains act as interaction hubs within modular polyketide synthase (PKS) systems, employing specific protein-protein interactions to present acyl substrates to a series of enzyme active sites. Many domains from the multimodular PKS that generates the toxin mycolactone display an unusually high degree of sequence similarity, implying that the few sites which vary may do so for functional reasons. When domain boundaries based on prior studies were used to prepare two isolated ACP segments from this system for studies of their interaction properties, one fragment adopted the expected tertiary structure, but the other failed to fold, despite sharing a sequence identity of 49%. Secondary structure prediction uncovered a previously undetected helical region (H0) that precedes the canonical helix-bundle ACP topology in both cases. This article reports the NMR solution structures of two N-terminally extended mycolactone mACP constructs, mH0ACPa and mH0ACPb, both of which possess an additional α-helix that behaves like a rigid component of the domain. The interactions of these species with a phosphopantetheinyl transferase and a ketoreductase domain are unaffected by the presence of H0, but a shorter construct that lacks the H0 region is shown to be substantially less thermostable than mH0ACPb. Bioinformatics analysis suggests that the extended H0-ACP motif is present in 98% of type I cis-acyltransferase PKS chain-extension modules. The polypeptide linker that connects an H0-ACP motif to the preceding domain must therefore be ~12 residues shorter than previously thought, imposing strict limits on ACP-mediated substrate delivery within and between PKS modules.
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Affiliation(s)
- Luisa Moretto
- Department of Chemistry and Biomedical Sciences, Linnaeus University, Smålandsgatan-24, 392 34, Kalmar, Sweden
| | - Rachel Heylen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Natalie Holroyd
- Department of Medical Physics and Bioengineering, University College London, London, WC1E 6BT, UK
| | - Steven Vance
- Crescendo Biologics Ltd, Meditrina Building 260, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - R William Broadhurst
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge, CB2 1GA, UK.
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32
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Ciemny MP, Badaczewska-Dawid AE, Pikuzinska M, Kolinski A, Kmiecik S. Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields. Int J Mol Sci 2019; 20:E606. [PMID: 30708941 PMCID: PMC6386871 DOI: 10.3390/ijms20030606] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 01/23/2019] [Accepted: 01/29/2019] [Indexed: 12/20/2022] Open
Abstract
The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling protein interactions, which involve disordered peptide partners or intrinsically disordered protein regions, and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein⁻peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein⁻peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution, and simulation of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.
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Affiliation(s)
- Maciej Pawel Ciemny
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland.
| | | | - Monika Pikuzinska
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Andrzej Kolinski
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
| | - Sebastian Kmiecik
- Faculty of Chemistry, Biological and Chemical Research Center, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland.
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Jin Y, Duan M, Wang X, Kong X, Zhou W, Sun H, Liu H, Li D, Yu H, Li Y, Hou T. Communication between the Ligand-Binding Pocket and the Activation Function-2 Domain of Androgen Receptor Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:842-857. [DOI: 10.1021/acs.jcim.8b00796] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ye Jin
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mojie Duan
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, China
| | - Xuwen Wang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xiaotian Kong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Wenfang Zhou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huiyong Sun
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Hui Liu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Huidong Yu
- Rongene Pharma Co., Ltd., Shenzhen, Guangdong 518054, China
| | - Youyong Li
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
| | - Tingjun Hou
- Institute of Functional Nano and Soft Materials (FUNSOM), Soochow University, Suzhou, Jiangsu 215123, China
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
- State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang 310058, China
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Li D, Zhou W, Pang J, Tang Q, Zhong B, Shen C, Xiao L, Hou T. A magic drug target: Androgen receptor. Med Res Rev 2018; 39:1485-1514. [PMID: 30569509 DOI: 10.1002/med.21558] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Revised: 11/20/2018] [Accepted: 11/26/2018] [Indexed: 12/18/2022]
Abstract
Androgen receptor (AR) is closely associated with a group of hormone-related diseases including the cancers of prostate, breast, ovary, pancreas, etc and anabolic deficiencies such as muscle atrophy and osteoporosis. Depending on the specific type and stage of the diseases, AR ligands including not only antagonists but also agonists and modulators are considered as potential therapeutics, which makes AR an extremely interesting drug target. Here, we at first review the current understandings on the structural characteristics of AR, and then address why and how AR is investigated as a drug target for the relevant diseases and summarize the representative antagonists and agonists targeting five prospective small molecule binding sites at AR, including ligand-binding pocket, activation function-2 site, binding function-3 site, DNA-binding domain, and N-terminal domain, providing recent insights from a target and drug development view. Further comprehensive studies on AR and AR ligands would bring fruitful information and push the therapy of AR relevant diseases forward.
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Affiliation(s)
- Dan Li
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Wenfang Zhou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jinping Pang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Qin Tang
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Bingling Zhong
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Chao Shen
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China
| | - Li Xiao
- School of Life Science, Huzhou University, Huzhou, China
| | - Tingjun Hou
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, China.,State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, China
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35
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Liu Y, Wu M, Wang T, Xie Y, Cui X, He L, He Y, Li X, Liu M, Hu L, Cen S, Zhou J. Structural Based Screening of Antiandrogen Targeting Activation Function-2 Binding Site. Front Pharmacol 2018; 9:1419. [PMID: 30555332 PMCID: PMC6284051 DOI: 10.3389/fphar.2018.01419] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 11/19/2018] [Indexed: 11/22/2022] Open
Abstract
Androgen receptor (AR) plays a critical role in the development and progression of prostate cancer (PCa). Current antiandrogen therapies induce resistant mutations at the hormone binding pocket (HBP) that convert the activity of these agents from antagonist to agonist. Thus, there is a high unmet medical need for the development of novel antiandrogens which circumvent mutation-based resistance. Herein, through the analysis of AR structures with ligands binding to the activation function-2 (AF2) site, we built a combined pharmacophore model. In silico screening and the subsequent biological evaluation lead to the discovery of the novel lead compound IMB-A6 that binds to the AF2 site, which inhibits the activity of either wild-type (WT) or resistance mutated ARs. Our work demonstrates structure-based drug design is an efficient strategy to discover new antiandrogens, and provides a new class of small molecular antiandrogens for the development of novel treatment agents against PCa.
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Affiliation(s)
- Yangguang Liu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Meng Wu
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianqi Wang
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yongli Xie
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiangling Cui
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Liujun He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Yang He
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaoyu Li
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Mingliang Liu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Laixing Hu
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Shan Cen
- Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
| | - Jinming Zhou
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, Department of Chemistry, Zhejiang Normal University, Jinhua, China.,Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences, Beijing, China
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36
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Roman BI, Guedes RC, Stevens CV, García-Sosa AT. Recovering Actives in Multi-Antitarget and Target Design of Analogs of the Myosin II Inhibitor Blebbistatin. Front Chem 2018; 6:179. [PMID: 29881723 PMCID: PMC5976736 DOI: 10.3389/fchem.2018.00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 05/04/2018] [Indexed: 11/18/2022] Open
Abstract
In multitarget drug design, it is critical to identify active and inactive compounds against a variety of targets and antitargets. Multitarget strategies thus test the limits of available technology, be that in screening large databases of compounds vs. a large number of targets, or in using in silico methods for understanding and reliably predicting these pharmacological outcomes. In this paper, we have evaluated the potential of several in silico approaches to predict the target, antitarget and physicochemical profile of (S)-blebbistatin, the best-known myosin II ATPase inhibitor, and a series of analogs thereof. Standard and augmented structure-based design techniques could not recover the observed activity profiles. A ligand-based method using molecular fingerprints was, however, able to select actives for myosin II inhibition. Using further ligand- and structure-based methods, we also evaluated toxicity through androgen receptor binding, affinity for an array of antitargets and the ADME profile (including assay-interfering compounds) of the series. In conclusion, in the search for (S)-blebbistatin analogs, the dissimilarity distance of molecular fingerprints to known actives and the computed antitarget and physicochemical profile of the molecules can be used for compound design for molecules with potential as tools for modulating myosin II and motility-related diseases.
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Affiliation(s)
- Bart I Roman
- Research Group SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium.,Cancer Research Institute Ghent Ghent, Belgium
| | - Rita C Guedes
- Department of Medicinal Chemistry, Faculty of Pharmacy, Research Institute for Medicines (iMed.ULisboa), Universidade de Lisboa Lisbon, Portugal
| | - Christian V Stevens
- Research Group SynBioC, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University Ghent, Belgium.,Cancer Research Institute Ghent Ghent, Belgium
| | - Alfonso T García-Sosa
- Department of Molecular Technology, Institute of Chemistry, University of Tartu Tartu, Estonia
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37
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Turan I, Kotan LD, Tastan M, Gurbuz F, Topaloglu AK, Yuksel B. Molecular genetic studies in a case series of isolated hypoaldosteronism due to biosynthesis defects or aldosterone resistance. Clin Endocrinol (Oxf) 2018; 88:799-805. [PMID: 29582446 DOI: 10.1111/cen.13603] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 03/21/2018] [Accepted: 03/21/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND AND AIM Hypoaldosteronism is associated with either insufficient aldosterone production or aldosterone resistance (pseudohypoaldosteronism). Patients with aldosterone defects typically present with similar symptoms and findings, which include failure to thrive, vomiting, hyponatremia, hyperkalemia and metabolic acidosis. Accurate diagnosis of these clinical conditions therefore can be challenging. Molecular genetic analyses can help to greatly clarify this complexity. The aim of this study was to obtain an overview of the clinical and genetic characteristics of patients with aldosterone defects due to biosynthesis defects or aldosterone resistance. DESIGN AND PATIENTS We investigated the clinical and molecular genetic features of 8 consecutive patients with a clinical picture of aldosterone defects seen in our clinics during the period of May 2015 through October 2017. We screened CYP11B2 for aldosterone synthesis defects and NR3C2 and the three EnaC subunits (SCNN1A, SCNN1B and SCNN1G) for aldosterone resistance. RESULTS We found 4 novel and 2 previously reported mutations in the genes CYP11B2, NR3C2, SCNN1A and SCNN1G in 9 affected individuals from 7 unrelated families. CONCLUSION Molecular genetic investigations can help confidently diagnose these conditions and clarify the pathogenicity of aldosterone defects. This study may expand the clinical and genetic correlations of defects in aldosterone synthesis or resistance.
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Affiliation(s)
- Ihsan Turan
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
| | - Leman Damla Kotan
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
| | - Mehmet Tastan
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
| | - Fatih Gurbuz
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
| | - Ali Kemal Topaloglu
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
| | - Bilgin Yuksel
- Faculty of Medicine, Division of Pediatric Endocrinology, Cukurova University, Adana, Turkey
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38
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Sakkiah S, Kusko R, Pan B, Guo W, Ge W, Tong W, Hong H. Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations. Front Pharmacol 2018; 9:492. [PMID: 29867496 PMCID: PMC5962723 DOI: 10.3389/fphar.2018.00492] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 04/25/2018] [Indexed: 01/28/2023] Open
Abstract
When a small molecule binds to the androgen receptor (AR), a conformational change can occur which impacts subsequent binding of co-regulator proteins and DNA. In order to accurately study this mechanism, the scientific community needs a crystal structure of the Wild type AR (WT-AR) ligand binding domain, bound with antagonist. To address this open need, we leveraged molecular docking and molecular dynamics (MD) simulations to construct a structure of the WT-AR ligand binding domain bound with antagonist bicalutamide. The structure of mutant AR (Mut-AR) bound with this same antagonist informed this study. After molecular docking analysis pinpointed the suitable binding orientation of a ligand in AR, the model was further optimized through 1 μs of MD simulations. Using this approach, three molecular systems were studied: (1) WT-AR bound with agonist R1881, (2) WT-AR bound with antagonist bicalutamide, and (3) Mut-AR bound with bicalutamide. Our structures were very similar to the experimentally determined structures of both WT-AR with R1881 and Mut-AR with bicalutamide, demonstrating the trustworthiness of this approach. In our model, when WT-AR is bound with bicalutamide, Val716/Lys720/Gln733, or Met734/Gln738/Glu897 move and thus disturb the positive and negative charge clumps of the AF2 site. This disruption of the AF2 site is key for understanding the impact of antagonist binding on subsequent co-regulator binding. In conclusion, the antagonist induced structural changes in WT-AR detailed in this study will enable further AR research and will facilitate AR targeting drug discovery.
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Affiliation(s)
- Sugunadevi Sakkiah
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Rebecca Kusko
- Immuneering Corporation, Cambridge, MA, United States
| | - Bohu Pan
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Wenjing Guo
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weigong Ge
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, United States
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Liu X, Gao Y, Ye H, Gerrin S, Ma F, Wu Y, Zhang T, Russo J, Cai C, Yuan X, Liu J, Chen S, Balk SP. Positive feedback loop mediated by protein phosphatase 1α mobilization of P-TEFb and basal CDK1 drives androgen receptor in prostate cancer. Nucleic Acids Res 2017; 45:3738-3751. [PMID: 28062857 PMCID: PMC5397168 DOI: 10.1093/nar/gkw1291] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 12/25/2016] [Indexed: 01/05/2023] Open
Abstract
P-TEFb (CDK9/cyclin T) plays a central role in androgen receptor (AR)-mediated transactivation by phosphorylating both RNA polymerase 2 complex proteins and AR at S81. CDK9 dephosphorylation mobilizes P-TEFb from an inhibitory 7SK ribonucleoprotein complex, but mechanisms targeting phosphatases to P-TEFb are unclear. We show that AR recruits protein phosphatase 1α (PP1α), resulting in P-TEFb mobilization and CDK9-mediated AR S81 phosphorylation. This increased pS81 enhances p300 recruitment, histone acetylation, BRD4 binding and subsequent further recruitment of P-TEFb, generating a positive feedback loop that sustains transcription. AR S81 is also phosphorylated by CDK1, and blocking basal CDK1-mediated S81 phosphorylation markedly suppresses AR activity and initiation of this positive feedback loop. Finally, androgen-independent AR activity in castration-resistant prostate cancer (CRPC) cells is driven by increased CDK1-mediated S81 phosphorylation. Collectively these findings reveal a mechanism involving PP1α, CDK9 and CDK1 that is used by AR to initiate and sustain P-TEFb activity, which may be exploited to drive AR in CRPC.
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Affiliation(s)
- Xiaming Liu
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yanfei Gao
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - HuiHui Ye
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Sean Gerrin
- Department of Pathology, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Fen Ma
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Yiming Wu
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Tengfei Zhang
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Joshua Russo
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Changmeng Cai
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Xin Yuan
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Jihong Liu
- Department of Urology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shaoyong Chen
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
| | - Steven P Balk
- Hematology-Oncology Division, Department of Medicine, Beth Israel Deaconess Medical Center and Harvard Medical School, Boston, MA 02215, USA
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40
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Characterization of a novel androgen receptor (AR) coregulator RIPK1 and related chemicals that suppress AR-mediated prostate cancer growth via peptide and chemical screening. Oncotarget 2017; 8:69508-69519. [PMID: 29050220 PMCID: PMC5642495 DOI: 10.18632/oncotarget.17843] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 04/27/2017] [Indexed: 11/25/2022] Open
Abstract
Using bicalutamide-androgen receptor (AR) DNA binding domain-ligand binding domain as bait, we observed enrichment of FxxFY motif-containing peptides. Protein database searches revealed the presence of receptor-interacting protein kinase 1 (RIPK1) harboring one FxxFY motif. RIPK1 interacted directly with AR and suppressed AR transactivation in a dose-dependent manner. Domain mapping experiments showed that the FxxFY motif in RIPK1 is critical for interactions with AR and the death domain of RIPK1 plays a crucial role in its inhibitory effect on transactivation. In terms of tissue expression, RIPK1 levels were markedly higher in benign prostate hyperplasia and non-cancerous tissue regions relative to the tumor area. With the aid of computer modeling for screening of chemicals targeting activation function 2 (AF-2) of AR, we identified oxadiazole derivatives as good candidates and subsequently generated a small library of these compounds. A number of candidates could effectively suppress AR transactivation and AR-related functions in vitro and in vivo with tolerable toxicity via inhibiting AR-peptide, AR-coregulator and AR N-C interactions. Combination of these chemicals with antiandrogen had an additive suppressive effect on AR transcriptional activity. Our collective findings may pave the way in creating new strategies for the development and design of anti-AR drugs.
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41
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Liao JM, Wang YT, Lin CLS. A fragment-based docking simulation for investigating peptide–protein bindings. Phys Chem Chem Phys 2017; 19:10436-10442. [DOI: 10.1039/c6cp07136h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We developed a fragment-based docking strategy for long peptide docking simulations, which separates a long peptide into halves for docking, and then recombined to rebuild whole-peptide docking conformations. With further screening, optimizations and MM/GBSA scoring, our method was capable of efficiently predicting the near-native peptide binding conformations.
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Affiliation(s)
- Jun-min Liao
- Graduate School of Medicine
- Kaohsiung Medical University
- Taiwan
| | - Yeng-Tseng Wang
- Department of Biochemistry
- Kaohsiung Medical University
- Taiwan
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42
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Ittiwut C, Pratuangdejkul J, Supornsilchai V, Muensri S, Hiranras Y, Sahakitrungruang T, Watcharasindhu S, Suphapeetiporn K, Shotelersuk V. Novel mutations of the SRD5A2 and AR genes in Thai patients with 46, XY disorders of sex development. J Pediatr Endocrinol Metab 2017; 30:19-26. [PMID: 27849622 DOI: 10.1515/jpem-2016-0048] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2016] [Accepted: 09/05/2016] [Indexed: 11/15/2022]
Abstract
BACKGROUND Abnormalities of dihydrotestosterone conversion [5α-reductase deficiency: online Mendelian inheritance in man (OMIM) 607306] or actions of androgens [partial androgen insensitivity syndrome (PAIS): OMIM 312300] during the 8th-12th weeks of gestation cause varying degrees of undervirilized external genitalia in 46, XY disorders of sex development (DSD) with increased testosterone production. The objective of the study was to determine clinical and genetic characteristics of Thai patients with 46, XY DSD. METHODS A cross-sectional study was conducted in 46, XY DSD with increased testosterone production (n=43) evaluated by a human chorionic gonadotropin (hCG) stimulation test or clinical features consistent with 5α-reductase deficiency or PAIS. PCR sequencing of the entire coding regions of the SRD5A2 and AR genes was performed. Molecular modeling analysis of the androgen receptor-ligand-binding domain (AR-LBD) of a novel mutation was constructed. RESULTS Mutations were found in seven patients (16.3%): five (11.6%) and two (4.7%) patients had mutations in SRD5A2 and AR, respectively. Two novel mutations, SRD5A2 c.383A>G (p.Y128C) and AR c.2176C>T (p.R726C), were identified. Dimensional structural analysis of the novel mutated AR (p.R726C) revealed that it affected the co-activator binding [binding function-3 (BF-3)], not the testosterone binding site. Short phallus length was associated with 5α-reductase deficiency. CONCLUSIONS Around 16.3% of our patients with 46, XY DSD had 5α-reductase deficiency or PAIS. Two novel mutations of SRD5A2 and AR were identified. The novel mutated AR (p.R726C) might affect the co-activator binding (BF-3), not the testosterone binding site.
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MESH Headings
- 3-Oxo-5-alpha-Steroid 4-Dehydrogenase/genetics
- Amino Acid Sequence
- Androgens/metabolism
- Biomarkers/metabolism
- Child
- Child, Preschool
- Cross-Sectional Studies
- Dihydrotestosterone/metabolism
- Disorder of Sex Development, 46,XY/genetics
- Disorder of Sex Development, 46,XY/metabolism
- Disorder of Sex Development, 46,XY/pathology
- Female
- Follow-Up Studies
- Humans
- Infant
- Male
- Membrane Proteins/genetics
- Mutation/genetics
- Prognosis
- Protein Conformation
- Receptors, Androgen/chemistry
- Receptors, Androgen/genetics
- Sequence Homology, Amino Acid
- Testosterone/metabolism
- Thailand
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43
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De Mol E, Fenwick RB, Phang CTW, Buzón V, Szulc E, de la Fuente A, Escobedo A, García J, Bertoncini CW, Estébanez-Perpiñá E, McEwan IJ, Riera A, Salvatella X. EPI-001, A Compound Active against Castration-Resistant Prostate Cancer, Targets Transactivation Unit 5 of the Androgen Receptor. ACS Chem Biol 2016; 11:2499-505. [PMID: 27356095 DOI: 10.1021/acschembio.6b00182] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Castration-resistant prostate cancer is the lethal condition suffered by prostate cancer patients that become refractory to androgen deprivation therapy. EPI-001 is a recently identified compound active against this condition that modulates the activity of the androgen receptor, a nuclear receptor that is essential for disease progression. The mechanism by which this compound exerts its inhibitory activity is however not yet fully understood. Here we show, by using high resolution solution nuclear magnetic resonance spectroscopy, that EPI-001 selectively interacts with a partially folded region of the transactivation domain of the androgen receptor, known as transactivation unit 5, that is key for the ability of prostate cells to proliferate in the absence of androgens, a distinctive feature of castration-resistant prostate cancer. Our results can contribute to the development of more potent and less toxic novel androgen receptor antagonists for treating this disease.
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Affiliation(s)
- Eva De Mol
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - R. Bryn Fenwick
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Christopher T. W. Phang
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Victor Buzón
- Departament
de Bioquímica i Biología Molecular, and Institute of
Biomedicine, University of Barcelona (IBUB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Elzbieta Szulc
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Alex de la Fuente
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Albert Escobedo
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Jesús García
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Carlos W. Bertoncini
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Eva Estébanez-Perpiñá
- Departament
de Bioquímica i Biología Molecular, and Institute of
Biomedicine, University of Barcelona (IBUB), Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Iain J. McEwan
- Institute
of Medical Sciences, School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, IMS Building, Foresterhill, Aberdeen AB25 2ZD, Scotland, United Kingdom
| | - Antoni Riera
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- Departament
de Química Orgànica, Universitat de Barcelona, Martí
i Franqués 1-11, 08028 Barcelona, Spain
| | - Xavier Salvatella
- Institute
for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
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Biron E, Bédard F. Recent progress in the development of protein-protein interaction inhibitors targeting androgen receptor-coactivator binding in prostate cancer. J Steroid Biochem Mol Biol 2016. [PMID: 26196120 DOI: 10.1016/j.jsbmb.2015.07.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The androgen receptor (AR) is a key regulator for the growth, differentiation and survival of prostate cancer cells. Identified as a primary target for the treatment of prostate cancer, many therapeutic strategies have been developed to attenuate AR signaling in prostate cancer cells. While frontline androgen-deprivation therapies targeting either the production or action of androgens usually yield favorable responses in prostate cancer patients, a significant number acquire treatment resistance. Known as the castration-resistant prostate cancer (CRPC), the treatment options are limited for this advanced stage. It has been shown that AR signaling is restored in CRPC due to many aberrant mechanisms such as AR mutations, amplification or expression of constitutively active splice-variants. Coregulator recruitment is a crucial regulatory step in AR signaling and the direct blockade of coactivator binding to AR offers the opportunity to develop therapeutic agents that would remain effective in prostate cancer cells resistant to conventional endocrine therapies. Structural analyses of the AR have identified key surfaces involved in protein-protein interaction with coregulators that have been recently used to design and develop promising AR-coactivator binding inhibitors. In this review we will discuss the design and development of small-molecule inhibitors targeting the AR-coactivator interactions for the treatment of prostate cancer.
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Affiliation(s)
- Eric Biron
- Faculty of Pharmacy and Centre de recherche en endocrinologie moléculaire et oncologique et génomique humaine, Université Laval, Canada; Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, G1 V 4G2, Québec, QC, Canada.
| | - François Bédard
- Faculty of Pharmacy and Centre de recherche en endocrinologie moléculaire et oncologique et génomique humaine, Université Laval, Canada; Laboratory of Medicinal Chemistry, CHU de Québec Research Centre, G1 V 4G2, Québec, QC, Canada
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Bryce AH, Antonarakis ES. Androgen receptor splice variant 7 in castration-resistant prostate cancer: Clinical considerations. Int J Urol 2016; 23:646-53. [PMID: 27255944 DOI: 10.1111/iju.13134] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 05/02/2016] [Indexed: 12/11/2022]
Abstract
Constitutively-active ligand-independent splice variants of the androgen receptor are an adaptive response by prostate cancer cells to escape androgen deprivation therapy and novel androgen receptor-directed treatments. Androgen receptor splice variant 7 is the most common splice variant detected in clinical biospecimens, and emerging data now suggest that the presence of tumoral androgen receptor splice variant 7 might be indicative of primary and acquired resistance to next-generation androgen pathway inhibitors, such as abiraterone and enzalutamide. At the same time, taxane chemotherapy might retain its efficacy regardless of androgen receptor splice variant 7 status, thus suggesting the potential for a predictive biomarker guiding treatment selection in men with metastatic castration-resistant prostate cancer. Herein, we review the preclinical data elucidating the structure and function of androgen receptor splice variant 7, we describe the existing clinical data using this biomarker in metastatic castration-resistant prostate cancer, and we highlight potential therapeutic strategies to target androgen receptor splice variant 7-expressing prostate cancer.
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Affiliation(s)
- Alan H Bryce
- Division of Hematology and Medical Oncology, Mayo Clinic, Scottsdale, Arizona, USA
| | - Emmanuel S Antonarakis
- Departments of Oncology and Urology, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
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Sakkiah S, Ng HW, Tong W, Hong H. Structures of androgen receptor bound with ligands: advancing understanding of biological functions and drug discovery. Expert Opin Ther Targets 2016; 20:1267-82. [PMID: 27195510 DOI: 10.1080/14728222.2016.1192131] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Androgen receptor (AR) is a ligand-dependent transcription factor and a member of the nuclear receptor superfamily. It plays a vital role in male sexual development and regulates gene expression in various tissues, including prostate. Androgens are compounds that exert their biological effects via interaction with AR. Binding of androgens to AR initiates conformational changes in AR that affect binding of co-regulator proteins and DNA. AR agonists and antagonists are widely used in a variety of clinical applications (i.e. hypogonadism and prostate cancer therapy). AREAS COVERED This review provides a close look at structures of AR-ligand complexes and mutations in the receptor that have been revealed, discusses current challenges in the field, and sheds light on future directions. EXPERT OPINION AR is one of the primary targets for the treatment of prostate cancer, as AR antagonists inhibit prostate cancer growth. However, these drugs are not effective for long-term treatment and lead to castration-resistant prostate cancer. The structures of AR-ligand complexes are an invaluable scientific asset that enhances our understanding of biological functions and mechanisms of androgenic and anti-androgenic chemicals as well as promotes the discovery of superior drug candidates.
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Affiliation(s)
- Sugunadevi Sakkiah
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Hui Wen Ng
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Weida Tong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
| | - Huixiao Hong
- a Division of Bioinformatics and Biostatistics , National Center for Toxicological Research, U.S. Food and Drug Administration , Jefferson , AR , USA
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Ogino Y, Kuraku S, Ishibashi H, Miyakawa H, Sumiya E, Miyagawa S, Matsubara H, Yamada G, Baker ME, Iguchi T. Neofunctionalization of Androgen Receptor by Gain-of-Function Mutations in Teleost Fish Lineage. Mol Biol Evol 2015; 33:228-44. [PMID: 26507457 DOI: 10.1093/molbev/msv218] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Steroid hormone receptor family provides an example of evolution of diverse transcription factors through whole-genome duplication (WGD). However, little is known about how their functions have been evolved after the duplication. Teleosts present a good model to investigate an accurate evolutionary history of protein function after WGD, because a teleost-specific WGD (TSGD) resulted in a variety of duplicated genes in modern fishes. This study focused on the evolution of androgen receptor (AR) gene, as two distinct paralogs, ARα and ARβ, have evolved in teleost lineage after TSGD. ARα showed a unique intracellular localization with a higher transactivation response than that of ARβ. Using site-directed mutagenesis and computational prediction of protein-ligand interactions, we identified two key substitutions generating a new functionality of euteleost ARα. The substitution in the hinge region contributes to the unique intracellular localization of ARα. The substitution on helices 10/11 in the ligand-binding domain possibly modulates hydrogen bonds that stabilize the receptor-ligand complex leading to the higher transactivation response of ARα. These substitutions were conserved in Acanthomorpha (spiny-rayed fish) ARαs, but not in an earlier branching lineage among teleosts, Japanese eel. Insertion of these substitutions into ARs from Japanese eel recapitulates the evolutionary novelty of euteleost ARα. These findings together indicate that the substitutions generating a new functionality of teleost ARα were fixed in teleost genome after the divergence of the Elopomorpha lineage. Our findings provide a molecular explanation for an adaptation process leading to generation of the hyperactive AR subtype after TSGD.
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Affiliation(s)
- Yukiko Ogino
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Shigehiro Kuraku
- Phyloinformatics Unit, RIKEN Center for Life Science Technologies, Kobe, Japan
| | - Hiroshi Ishibashi
- Department of Life Environmental Conservation, Faculty of Agriculture, Ehime University, Matsuyama, Japan
| | - Hitoshi Miyakawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Eri Sumiya
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Shinichi Miyagawa
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
| | - Hajime Matsubara
- Department of Aquatic Biology, Faculty of Bioindustry, Tokyo University of Agriculture, Abashiri, Japan
| | - Gen Yamada
- Department of Developmental Genetics, Institute of Advanced Medicine, Wakayama Medical University, Wakayama, Japan
| | | | - Taisen Iguchi
- Okazaki Institute for Integrative Bioscience, National Institute for Basic Biology, National Institutes of Natural Sciences, and Department of Basic Biology, SOKENDAI (The Graduate University for Advanced Studies), Okazaki, Japan
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Brooke GN, Powell SM, Lavery DN, Waxman J, Buluwela L, Ali S, Bevan CL. Engineered repressors are potent inhibitors of androgen receptor activity. Oncotarget 2015; 5:959-69. [PMID: 24659630 PMCID: PMC4011597 DOI: 10.18632/oncotarget.1360] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Prostate cancer growth is dependent upon the Androgen Receptor (AR) pathway, hence therapies for this disease often target this signalling axis. Such therapies are successful in the majority of patients but invariably fail after a median of 2 years and tumours progress to a castrate resistant stage (CRPC). Much evidence exists to suggest that the AR remains key to CRPC growth and hence remains a valid therapeutic target. Here we describe a novel method to inhibit AR activity, consisting of an interaction motif, that binds to the AR ligand-binding domain, fused to repression domains. These ‘engineered repressors’ are potent inhibitors of AR activity and prostate cancer cell growth and importantly inhibit the AR under circumstances in which conventional therapies would be predicted to fail, such as AR mutation and altered cofactor levels.
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Affiliation(s)
- Greg N Brooke
- Department of Surgery and Cancer, Imperial Centre for Translational and Experimental Medicine, Imperial College London, W12 0NN, UK
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Brooke GN, Gamble SC, Hough MA, Begum S, Dart DA, Odontiadis M, Powell SM, Fioretti FM, Bryan RA, Waxman J, Wait R, Bevan CL. Antiandrogens act as selective androgen receptor modulators at the proteome level in prostate cancer cells. Mol Cell Proteomics 2015; 14:1201-16. [PMID: 25693800 PMCID: PMC4424393 DOI: 10.1074/mcp.m113.036764] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Indexed: 11/06/2022] Open
Abstract
Current therapies for prostate cancer include antiandrogens, inhibitory ligands of the androgen receptor, which repress androgen-stimulated growth. These include the selective androgen receptor modulators cyproterone acetate and hydroxyflutamide and the complete antagonist bicalutamide. Their activity is partly dictated by the presence of androgen receptor mutations, which are commonly detected in patients who relapse while receiving antiandrogens, i.e. in castrate-resistant prostate cancer. To characterize the early proteomic response to these antiandrogens we used the LNCaP prostate cancer cell line, which harbors the androgen receptor mutation most commonly detected in castrate-resistant tumors (T877A), analyzing alterations in the proteome, and comparing these to the effect of these therapeutics upon androgen receptor activity and cell proliferation. The majority are regulated post-transcriptionally, possibly via nongenomic androgen receptor signaling. Differences detected between the exposure groups demonstrate subtle changes in the biological response to each specific ligand, suggesting a spectrum of agonistic and antagonistic effects dependent on the ligand used. Analysis of the crystal structures of the AR in the presence of cyproterone acetate, hydroxyflutamide, and DHT identified important differences in the orientation of key residues located in the AF-2 and BF-3 protein interaction surfaces. This further implies that although there is commonality in the growth responses between androgens and those antiandrogens that stimulate growth in the presence of a mutation, there may also be influential differences in the growth pathways stimulated by the different ligands. This therefore has implications for prostate cancer treatment because tumors may respond differently dependent upon which mutation is present and which ligand is activating growth, also for the design of selective androgen receptor modulators, which aim to elicit differential proteomic responses dependent upon cellular context.
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Affiliation(s)
- Greg N Brooke
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK; §Molecular Oncology, School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Simon C Gamble
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK
| | - Michael A Hough
- §Molecular Oncology, School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Shajna Begum
- ¶Kennedy Institute of Rheumatology, Imperial College London, London W6 8LH, UK
| | - D Alwyn Dart
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK; ‖Cardiff University Peking University Cancer Institute, Cardiff University School of Medicine, Cardiff CF14 4XN, UK
| | - Michael Odontiadis
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK
| | - Sue M Powell
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK
| | - Flavia M Fioretti
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK
| | - Rosie A Bryan
- §Molecular Oncology, School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Jonathan Waxman
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK
| | - Robin Wait
- ¶Kennedy Institute of Rheumatology, Imperial College London, London W6 8LH, UK
| | - Charlotte L Bevan
- From the ‡Androgen Signalling Laboratory, Imperial College London, London W12 0NN, UK;
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