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Hao X, Wang Y, Hou MJ, Liao L, Yang YX, Wang YH, Zhu BT. Raloxifene Prevents Chemically-Induced Ferroptotic Neuronal Death In Vitro and In Vivo. Mol Neurobiol 2024:10.1007/s12035-024-04497-7. [PMID: 39354232 DOI: 10.1007/s12035-024-04497-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 09/12/2024] [Indexed: 10/03/2024]
Abstract
Ferroptosis, a regulated form of cell death characterized by excessive iron-dependent lipid peroxidation, can be readily induced in cultured cells by chemicals such as erastin and RSL3. Protein disulfide isomerase (PDI) has been identified as an upstream mediator of chemically induced ferroptosis and also a target for ferroptosis protection. In this study, we discovered that raloxifene (RAL), a selective estrogen receptor modulator known for its neuroprotective actions in humans, can effectively inhibit PDI function and provide robust protection against chemically induced ferroptosis in cultured HT22 neuronal cells. Specifically, RAL can bind directly to PDI both in vitro and in intact neuronal cells and inhibit its catalytic activity. Computational modeling analysis reveals that RAL can tightly bind to PDI through forming a hydrogen bond with its His256 residue, and biochemical analysis further shows that when PDI's His256 is mutated to Ala256, RAL loses its inhibition of PDI's catalytic activity. This inhibition of PDI by RAL significantly reduces the dimerization of both the inducible and neuronal nitric oxide synthases and the accumulation of nitric oxide, both of which have recently been shown to play a crucial role in mediating chemically induced ferroptosis through subsequent induction of ROS and lipid-ROS accumulation. In vivo behavioral analysis shows that mice treated with RAL are strongly protected against kainic acid-induced memory deficits and hippocampal neuronal damage. In conclusion, this study demonstrates that RAL is a potent inhibitor of PDI and can effectively prevent chemically induced ferroptosis in hippocampal neurons both in vitro and in vivo. These findings offer a novel estrogen receptor-independent mechanism for RAL's neuroprotective actions in animal models and humans.
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Affiliation(s)
- Xiangyu Hao
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China
| | - Yifan Wang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China
| | - Ming-Jie Hou
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China
| | - Lixi Liao
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China
| | - Yong Xiao Yang
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China
| | - Ying-Hua Wang
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bao Ting Zhu
- Shenzhen Key Laboratory of Steroid Drug Discovery and Development, School of Medicine, The Chinese University of Hong Kong (Shenzhen), 2001 Longxiang Road, Longgang District, Shenzhen, 518,172, China.
- Shenzhen Bay Laboratory, Shenzhen, 518,055, China.
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2
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Chauhan SS, Garg P, Parthasarathi R. Computational framework for identifying and evaluating mutagenic and xenoestrogenic potential of food additives. JOURNAL OF HAZARDOUS MATERIALS 2024; 470:134233. [PMID: 38603913 DOI: 10.1016/j.jhazmat.2024.134233] [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: 11/13/2023] [Revised: 03/23/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024]
Abstract
Food additives are chemicals incorporated in food to enhance its flavor, color and prevent spoilage. Some of these are associated with substantial health hazards, including developmental disorders, increase cancer risk, and hormone disruption. Hence, this study aimed to comprehend the in-silico toxicology framework for evaluating mutagenic and xenoestrogenic potential of food additives and their association with breast cancer. A total of 2885 food additives were screened for toxicity based on Threshold of Toxicological Concern (TTC), mutagenicity endpoint prediction, and mutagenic structural alerts/toxicophores identification. Ten food additives were identified as having mutagenic potential based on toxicity screening. Furthermore, Protein-Protein Interaction (PPI) analysis identified ESR1, as a key hub gene in breast cancer. KEGG pathway analysis verified that ESR1 plays a significant role in breast cancer pathogenesis. Additionally, competitive interaction studies of the predicted potential mutagenic food additives with the estrogen receptor-α were evaluated at agonist and antagonist binding sites. Indole, Dichloromethane, Trichloroethylene, Quinoline, 6-methyl quinoline, Ethyl nitrite, and 4-methyl quinoline could act as agonists, and Paraldehyde, Azodicarbonamide, and 2-acetylfuranmay as antagonists. The systematic risk assessment framework reported in this study enables the exploration of mutagenic and xenoestrogenic potential associated with food additives for hazard identification and management.
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Affiliation(s)
- Shweta Singh Chauhan
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR, Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prekshi Garg
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR, Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India
| | - Ramakrishnan Parthasarathi
- Computational Toxicology Facility, Toxicoinformatics & Industrial Research, CSIR, Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow, Uttar Pradesh 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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3
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Hazarika S, Fehrle M, Okafor CD. How nuclear receptors transition between active and inactive forms: An energetic perspective. J Chem Phys 2024; 160:115102. [PMID: 38501469 DOI: 10.1063/5.0189234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Nuclear receptors regulate transcriptional programs in response to the binding of natural and synthetic ligands. These ligands modulate the receptor by inducing dynamic changes in the ligand binding domain that shift the C-terminal helix (H12) between active and inactive conformations. Despite decades of study, many questions persist regarding the nature of the inactive state and how ligands shift receptors between different states. Here, we use molecular dynamics (MD) simulations to investigate the timescale and energetic landscape of the conformational transition between inactive and active forms of progesterone receptor (PR) bound to a partial agonist. We observe that the microsecond timescale is insufficient to observe any transitions; only at millisecond timescales achieved via accelerated MD simulations do we find the inactive PR switches to the active state. Energetic analysis reveals that both active and inactive PR states represent energy minima separated by a barrier that can be traversed. In contrast, little or no transition is observed between active and inactive states when an agonist or antagonist is bound, confirming that ligand identity plays a key role in defining the energy landscape of nuclear receptor conformations.
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Affiliation(s)
- Saurov Hazarika
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Matthew Fehrle
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - C Denise Okafor
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA
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4
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Beheshtizadeh N, Gharibshahian M, Bayati M, Maleki R, Strachan H, Doughty S, Tayebi L. Vascular endothelial growth factor (VEGF) delivery approaches in regenerative medicine. Biomed Pharmacother 2023; 166:115301. [PMID: 37562236 DOI: 10.1016/j.biopha.2023.115301] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/28/2023] [Accepted: 08/05/2023] [Indexed: 08/12/2023] Open
Abstract
The utilization of growth factors in the process of tissue regeneration has garnered significant interest and has been the subject of extensive research. However, despite the fervent efforts invested in recent clinical trials, a considerable number of these studies have produced outcomes that are deemed unsatisfactory. It is noteworthy that the trials that have yielded the most satisfactory outcomes have exhibited a shared characteristic, namely, the existence of a mechanism for the regulated administration of growth factors. Despite the extensive exploration of drug delivery vehicles and their efficacy in delivering certain growth factors, the development of a reliable predictive approach for the delivery of delicate growth factors like Vascular Endothelial Growth Factor (VEGF) remains elusive. VEGF plays a crucial role in promoting angiogenesis; however, the administration of VEGF demands a meticulous approach as it necessitates precise localization and transportation to a specific target tissue. This process requires prolonged and sustained exposure to a low concentration of VEGF. Inaccurate administration of drugs, either through off-target effects or inadequate delivery, may heighten the risk of adverse reactions and potentially result in tumorigenesis. At present, there is a scarcity of technologies available for the accurate encapsulation of VEGF and its subsequent sustained and controlled release. The objective of this review is to present and assess diverse categories of VEGF administration mechanisms. This paper examines various systems, including polymeric, liposomal, hydrogel, inorganic, polyplexes, and microfluidic, and evaluates the appropriate dosage of VEGF for multiple applications.
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Affiliation(s)
- Nima Beheshtizadeh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Iran; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Maliheh Gharibshahian
- Department of Tissue Engineering, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran; Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Mohammad Bayati
- Department of Phytochemistry, Medicinal Plants and Drugs Research Institute, Shahid Beheshti University, Tehran, Iran
| | - Reza Maleki
- Department of Chemical Technologies, Iranian Research Organization for Science and Technology (IROST), P.O. Box 33535111, Tehran, Iran.
| | - Hannah Strachan
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
| | - Sarah Doughty
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
| | - Lobat Tayebi
- Marquette University School of Dentistry, Milwaukee, WI 53233, USA
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5
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Frkic RL, Pederick JL, Horsfall AJ, Jovcevski B, Crame EE, Kowalczyk W, Pukala TL, Chang MR, Zheng J, Blayo AL, Abell AD, Kamenecka TM, Harbort JS, Harmer JR, Griffin PR, Bruning JB. PPARγ Corepression Involves Alternate Ligand Conformation and Inflation of H12 Ensembles. ACS Chem Biol 2023; 18:1115-1123. [PMID: 37146157 DOI: 10.1021/acschembio.2c00917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Inverse agonists of peroxisome proliferator activated receptor γ (PPARγ) have emerged as safer alternatives to full agonists for their reduced side effects while still maintaining impressive insulin-sensitizing properties. To shed light on their molecular mechanism, we characterized the interaction of the PPARγ ligand binding domain with SR10221. X-ray crystallography revealed a novel binding mode of SR10221 in the presence of a transcriptionally repressing corepressor peptide, resulting in much greater destabilization of the activation helix, H12, than without corepressor peptide. Electron paramagnetic resonance provided in-solution complementary protein dynamic data, which revealed that for SR10221-bound PPARγ, H12 adopts a plethora of conformations in the presence of corepressor peptide. Together, this provides the first direct evidence for corepressor-driven ligand conformation for PPARγ and will allow the development of safer and more effective insulin sensitizers suitable for clinical use.
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Affiliation(s)
- Rebecca L Frkic
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jordan L Pederick
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elise E Crame
- Discipline of Physiology, School of Biomedicine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | | | - Tara L Pukala
- Department of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Mi Ra Chang
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Jie Zheng
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Anne-Laure Blayo
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Andrew D Abell
- ARC Centre of Excellence for Nanoscale Biophotonics, The Institute for Photonics and Advanced Sensing, and School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Theodore M Kamenecka
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - Joshua S Harbort
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Jeffrey R Harmer
- Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Patrick R Griffin
- Department of Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, Florida 33458, United States
- Department of Molecular Therapeutics, UF Scripps Biomolecular Research, University of Florida, Jupiter, Florida 33458, United States
| | - John B Bruning
- The Institute for Photonics and Advanced Sensing and School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
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6
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Clusan L, Percevault F, Jullion E, Le Goff P, Tiffoche C, Fernandez-Calero T, Métivier R, Marin M, Pakdel F, Michel D, Flouriot G. Codon adaptation by synonymous mutations impacts the functional properties of the estrogen receptor-alpha protein in breast cancer cells. Mol Oncol 2023. [PMID: 36808875 DOI: 10.1002/1878-0261.13399] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 01/30/2023] [Accepted: 02/16/2023] [Indexed: 02/23/2023] Open
Abstract
Oestrogen receptor-alpha (ERα) positivity is intimately associated with the development of hormone-dependent breast cancers. A major challenge in the treatment of these cancers is to understand and overcome the mechanisms of endocrine resistance. Recently, two distinct translation programmes using specific transfer RNA (tRNA) repertoires and codon usage frequencies were evidenced during cell proliferation and differentiation. Considering the phenotype switch of cancer cells to more proliferating and less-differentiated states, we can speculate that the changes in the tRNA pool and codon usage that likely occur make the ERα coding sequence no longer adapted, impacting translational rate, co-translational folding and the resulting functional properties of the protein. To verify this hypothesis, we generated an ERα synonymous coding sequence whose codon usage was optimized to the frequencies observed in genes expressed specifically in proliferating cells and then investigated the functional properties of the encoded receptor. We demonstrate that such a codon adaptation restores ERα activities to levels observed in differentiated cells, including: (a) an enhanced contribution exerted by transactivation function 1 (AF1) in ERα transcriptional activity; (b) enhanced interactions with nuclear receptor corepressor 1 and 2 [NCoR1 and NCoR2 (also known as SMRT) respectively], promoting repressive capability; and (c) reduced interactions with SRC proto-oncogene, non-receptor tyrosine kinase (Src) and phosphoinositide 3-kinase (PI3K) p85 kinases, inhibiting MAPK and AKT signalling pathway.
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Affiliation(s)
- Léa Clusan
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Frederic Percevault
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Emmanuelle Jullion
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Pascale Le Goff
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Christophe Tiffoche
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Tamara Fernandez-Calero
- Departamento de Ciencias Exactas Y Naturales, Universidad Catolica del Uruguay, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur Montevideo, Uruguay
| | - Raphaël Métivier
- Institut de Génétique De Rennes (IGDR), UMR 6290 CNRS, ERL INSERM U1305, Univ Rennes, France
| | - Monica Marin
- Biochemistry-Molecular Biology, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Farzad Pakdel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Denis Michel
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
| | - Gilles Flouriot
- Univ Rennes, Inserm, EHESP, Irset (Institut de Recherche en Santé, Environnement et Travail), UMR_S1085, France
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7
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Rikken G, Smith KJ, van den Brink NJM, Smits JPH, Gowda K, Alnemri A, Kuzu GE, Murray IA, Lin JM, Smits JGA, van Vlijmen-Willems IM, Amin SG, Perdew GH, van den Bogaard EH. Lead optimization of aryl hydrocarbon receptor ligands for treatment of inflammatory skin disorders. Biochem Pharmacol 2023; 208:115400. [PMID: 36574884 DOI: 10.1016/j.bcp.2022.115400] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/26/2022]
Abstract
Therapeutic aryl hydrocarbon receptor (AHR) modulating agents gained attention in dermatology as non-steroidal anti-inflammatory drugs that improve skin barrier properties. By exploiting AHR's known ligand promiscuity, we generated novel AHR modulating agents by lead optimization of a selective AHR modulator (SAhRM; SGA360). Twenty-two newly synthesized compounds were screened yielding two novel derivatives, SGA360f and SGA388, in which agonist activity led to enhanced keratinocyte terminal differentiation. SGA388 showed the highest agonist activity with potent normalization of keratinocyte hyperproliferation, restored expression of skin barrier proteins and dampening of chemokine expression by keratinocytes upon Th2-mediated inflammation in vitro. The topical application of SGA360f and SGA388 reduced acute skin inflammation in vivo by reducing cyclooxygenase levels, resulting in less neutrophilic dermal infiltrates. The minimal induction of cytochrome P450 enzyme activity, lack of cellular toxicity and mutagenicity classifies SGA360f and SGA388 as novel potential therapeutic AHR ligands and illustrates the potential of medicinal chemistry to fine-tune AHR signaling for the development of targeted therapies in dermatology and beyond.
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Affiliation(s)
- Gijs Rikken
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Kayla J Smith
- Department of Veterinary and Biomedical Sciences, and Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Noa J M van den Brink
- Department of Pharmacology, Penn State College of Medicine, Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Jos P H Smits
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Krishne Gowda
- Department of Pharmacology, Penn State College of Medicine, Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Angela Alnemri
- Department of Veterinary and Biomedical Sciences, and Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Gulsum E Kuzu
- Department of Veterinary and Biomedical Sciences, and Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Iain A Murray
- Department of Veterinary and Biomedical Sciences, and Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA
| | - Jyh-Ming Lin
- Metabolomics Facility, The Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
| | - Jos G A Smits
- Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University, Nijmegen, the Netherlands
| | - Ivonne M van Vlijmen-Willems
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands
| | - Shantu G Amin
- Department of Pharmacology, Penn State College of Medicine, Department of Biochemistry and Molecular Biology, Penn State College of Medicine, Hershey, PA, USA
| | - Gary H Perdew
- Department of Veterinary and Biomedical Sciences, and Center for Molecular Toxicology and Carcinogenesis, Penn State University, University Park, PA, USA.
| | - Ellen H van den Bogaard
- Department of Dermatology, Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Nijmegen, the Netherlands.
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8
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Kumari A, Mittal L, Srivastava M, Pathak DP, Asthana S. Deciphering the Structural Determinants Critical in Attaining the FXR Partial Agonism. J Phys Chem B 2023; 127:465-485. [PMID: 36609158 DOI: 10.1021/acs.jpcb.2c06325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Elucidation of structural determinants is pivotal for structure-based drug discovery. The Farnesoid X receptor (FXR) is a proven target for NASH; however, its full agonism causes certain clinical complications. Therefore, partial agonism (PA) appears as a viable alternative for improved therapeutics. Since the agonist and PA both share the same binding site, i.e., ligand-binding pocket (LBP), which is highly dynamic and has synergy with the substrate binding site, the selective designing of PA is challenging. The identification of structural and conformational determinants is critical for PA compared with an agonist. Furthermore, the mechanism by which PA modulates the structural dynamics of FXR at the residue level, a prerequisite for PA designing, is still elusive. Here, by using ∼4.5 μs of MD simulations and residue-wise communication network analysis, we identified the structural regions which are flexible with PA but frozen with an agonist. Also, the network analysis identified the considerable changes between an agonist and PA in biologically essential zones of FXR such as helix H10/H11 and loop L:H11/H12, which lead to the modulation of synergy between LBP and the substrate binding site. Furthermore, the thermodynamic profiling suggested the methionine residues, mainly M328, M365, and M450, seem to be responsible for the recruitment of PA. The other residues I357, Y361, L465, F308, Q316, and K321 are also identified, exclusively interacting with PA. This study offers novel structural and mechanistic insights that are critical for FXR targeted drug discovery for PA designing.
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Affiliation(s)
- Anita Kumari
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India.,Delhi Pharmaceutical Sciences and Research University (DPSRU), New Delhi110017, India
| | - Lovika Mittal
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Mitul Srivastava
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
| | - Dharam Pal Pathak
- Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), New Delhi110017, India
| | - Shailendra Asthana
- Translational Health Science and Technology Institute (THSTI), Faridabad, Haryana121001, India
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9
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Tinivella A, Nwachukwu JC, Angeli A, Foschi F, Benatti AL, Pinzi L, Izard T, Ferraroni M, Erumbi R, Christodoulou MS, Passarella D, Supuran CT, Nettles KW, Rastelli G. Design, synthesis, biological evaluation and crystal structure determination of dual modulators of carbonic anhydrases and estrogen receptors. Eur J Med Chem 2023; 246:115011. [PMID: 36516582 DOI: 10.1016/j.ejmech.2022.115011] [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: 11/06/2022] [Revised: 11/28/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
Multi-target compounds have become increasingly important for the development of safer and more effective drug candidates. In this work, we devised a combined ligand-based and structure-based multi-target repurposing strategy and applied it to a series of hexahydrocyclopenta[c]quinoline compounds synthesized previously. The in silico analyses identified human Carbonic Anhydrases (hCA) and Estrogen Receptors (ER) as top scoring candidates for dual modulation. hCA isoforms IX and XII, and ER subtypes ER⍺ and/or ERβ are co-expressed in various cancer cell types, including breast and prostate cancer cells. ER⍺ is the primary target of anti-estrogen therapy in breast cancer, and the hCA IX isoform is a therapeutic target in triple-negative breast cancer. ER⍺-mediated transcriptional programs and hCA activity in cancer cells promote favorable microenvironments for cell proliferation. Interestingly, several lines of evidence indicate that the combined modulation of these two targets may provide significant therapeutic benefits. Moving from these first results, two additional hexahydrocyclopenta[c]quinoline derivatives bearing a sulfonamide zinc binding group (hCA) and a phenolic hydroxyl (ER) pharmacophoric group placed at the appropriate locations were designed and synthesized. Interestingly, these compounds were able to directly modulate the activities of both hCA and ER targets. In cell-based assays, they inhibited proliferation of breast and prostate cancer cells with micromolar potency and cell type-selective efficacy. The compounds inhibited hCA activity with nanomolar potency and isoform-selectivity. In transactivation assays, they reduced estrogen-driven ER activity with micro-molar potency. Finally, crystal structures of the synthesized ligands in complex with the two targets revealed that the compounds bind directly to the hCA active site, as well as to the ER ligand-binding domain, providing structural explanation to the observed activity and a rationale for optimization of their dual activity. To the best of our knowledge, this work describes the design, synthesis and biological characterization of the first dual modulators of hCA and ER, laying the ground for the structure-based optimization of their multi-target activity.
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Affiliation(s)
- Annachiara Tinivella
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Clinical and Experimental Medicine PhD Program, University of Modena and Reggio Emilia, Modena, Italy
| | - Jerome C Nwachukwu
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Andrea Angeli
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Francesca Foschi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Anna Laura Benatti
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Luca Pinzi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy
| | - Tina Izard
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Marta Ferraroni
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 13, 50019, Sesto Fiorentino, Florence, Italy
| | - Rangarajan Erumbi
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Michael S Christodoulou
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy; Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Daniele Passarella
- Department of Chemistry, University of Milano, Via Golgi 19, 20133, Milano, Italy
| | - Claudiu T Supuran
- NEUROFARBA Department, Sezione di Scienze Farmaceutiche, University of Florence, Via Ugo Schiff 6, 50019, Sesto Fiorentino, Florence, Italy
| | - Kendall W Nettles
- Department of Integrative Structural and Computational Biology, University of Florida Scripps Biomedical Research, 130 Scripps Way, Jupiter, FL, 33458, USA
| | - Giulio Rastelli
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Giuseppe Campi 103, 41125, Modena, Italy.
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10
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Zengin G, Uba AI, Ocal M, Sharifi-Rad M, Caprioli G, Angeloni S, Altunoglu YC, Baloglu MC, Yıldıztugay E. Integration of in vitro and in silico approaches to assess three Astragalus species from Turkey flora: A novel spotlight from lab bench to functional applications. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2022.101858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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11
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Zhou Y, Gu B, Brichant G, Singh JP, Yang H, Chang H, Zhao Y, Cheng C, Liu ZW, Alderman MH, Lu L, Yang X, Gao XB, Taylor HS. The steroid hormone estriol (E3) regulates epigenetic programming of fetal mouse brain and reproductive tract. BMC Biol 2022; 20:93. [PMID: 35491423 PMCID: PMC9059368 DOI: 10.1186/s12915-022-01293-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 04/11/2022] [Indexed: 12/13/2022] Open
Abstract
Abstract
Background
Estriol (E3) is a steroid hormone formed only during pregnancy in primates including humans. Although E3 is synthesized at large amounts through a complex pathway involving the fetus and placenta, it is not required for the maintenance of pregnancy and has classically been considered virtually inactive due to associated very weak canonical estrogen signaling. However, estrogen exposure during pregnancy may have an effect on organs both within and outside the reproductive system, and compounds with binding affinity for estrogen receptors weaker than E3 have been found to impact reproductive organs and the brain. Here, we explore potential effects of E3 on fetal development using mouse as a model system.
Results
We administered E3 to pregnant mice, exposing the fetus to E3. Adult females exposed to E3 in utero (E3-mice) had increased fertility and superior pregnancy outcomes. Female and male E3-mice showed decreased anxiety and increased exploratory behavior. The expression levels and DNA methylation patterns of multiple genes in the uteri and brains of E3-mice were distinct from controls. E3 promoted complexing of estrogen receptors with several DNA/histone modifiers and their binding to target genes. E3 functions by driving epigenetic change, mediated through epigenetic modifier interactions with estrogen receptors rather than through canonical nuclear transcriptional activation.
Conclusions
We identify an unexpected functional role for E3 in fetal reproductive system and brain. We further identify a novel mechanism of estrogen action, through recruitment of epigenetic modifiers to estrogen receptors and their target genes, which is not correlated with the traditional view of estrogen potency.
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12
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Akermi S, Smaoui S, Elhadef K, Fourati M, Louhichi N, Chaari M, Chakchouk Mtibaa A, Baanannou A, Masmoudi S, Mellouli L. Cupressus sempervirens Essential Oil: Exploring the Antibacterial Multitarget Mechanisms, Chemcomputational Toxicity Prediction, and Safety Assessment in Zebrafish Embryos. Molecules 2022; 27:2630. [PMID: 35565980 PMCID: PMC9103706 DOI: 10.3390/molecules27092630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 12/11/2022] Open
Abstract
Nowadays, increasing interest has recently been given to the exploration of new food preservatives to avoid foodborne outbreaks or food spoilage. Likewise, new compounds that substitute the commonly used synthetic food preservatives are required to restrain the rising problem of microbial resistance. Accordingly, the present study was conducted to examine the chemical composition and the mechanism(s) of action of the Cupressus sempervirens essential oil (CSEO) against Salmonella enterica Typhimuriumand Staphyloccocus aureus. The gas chromatography analysis revealed α-pinene (38.47%) and δ-3-carene (25.14%) are the major components of the CSEO. By using computational methods, such as quantitative structure-activity relationship (QSAR), we revealed that many CSEO components had no toxic effects. Moreover, findings indicated that α-pinene, δ-3-carene and borneol, a minor compound of CSEO, could inhibit the AcrB-TolC and MepR efflux pump activity of S. enterica Typhimurium and S. aureus, respectively. In addition, our molecular docking predictions indicated the high affinity of these three compounds with active sites of bacterial DNA and RNA polymerases, pointing to plausible impairments of the pathogenic bacteria cell replication processes. As well, the safety profile was developed through the zebrafish model. The in vivo toxicological evaluation of (CSEO) exhibited a concentration-dependent manner, with a lethal concentration (LC50) equal to 6.6 µg/mL.
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Affiliation(s)
- Sarra Akermi
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Slim Smaoui
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Khaoula Elhadef
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Mariam Fourati
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Nacim Louhichi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (N.L.); (A.B.); (S.M.)
| | - Moufida Chaari
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Ahlem Chakchouk Mtibaa
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
| | - Aissette Baanannou
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (N.L.); (A.B.); (S.M.)
| | - Saber Masmoudi
- Laboratory of Molecular and Cellular Screening Processes, Center of Biotechnology of Sfax, University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (N.L.); (A.B.); (S.M.)
| | - Lotfi Mellouli
- Laboratory of Microbial Biotechnology and Engineering Enzymes (LMBEE), Center of Biotechnology of Sfax (CBS), University of Sfax, Road of Sidi Mansour Km 6, P.O. Box 1177, Sfax 3018, Tunisia; (S.A.); (K.E.); (M.F.); (M.C.); (A.C.M.); (L.M.)
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13
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Habibi N, Mauser A, Ko Y, Lahann J. Protein Nanoparticles: Uniting the Power of Proteins with Engineering Design Approaches. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104012. [PMID: 35077010 PMCID: PMC8922121 DOI: 10.1002/advs.202104012] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/12/2021] [Indexed: 05/16/2023]
Abstract
Protein nanoparticles, PNPs, have played a long-standing role in food and industrial applications. More recently, their potential in nanomedicine has been more widely pursued. This review summarizes recent trends related to the preparation, application, and chemical construction of nanoparticles that use proteins as major building blocks. A particular focus has been given to emerging trends related to applications in nanomedicine, an area of research where PNPs are poised for major breakthroughs as drug delivery carriers, particle-based therapeutics or for non-viral gene therapy.
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Affiliation(s)
- Nahal Habibi
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Ava Mauser
- Biointerfaces InstituteDepartment of Biomedical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Yeongun Ko
- Biointerfaces InstituteDepartment of Chemical EngineeringUniversity of MichiganAnn ArborMI48109USA
| | - Joerg Lahann
- Biointerfaces InstituteDepartments of Chemical EngineeringMaterial Science and EngineeringBiomedical Engineeringand Macromolecular Science and EngineeringUniversity of MichiganAnn ArborMI48109USA
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14
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Molecular profiling of ginsenoside metabolites to identify estrogen receptor alpha activity. Gene 2021; 813:146108. [PMID: 34929341 DOI: 10.1016/j.gene.2021.146108] [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: 03/09/2021] [Revised: 10/30/2021] [Accepted: 11/16/2021] [Indexed: 11/04/2022]
Abstract
20(S)-Protopanaxadiol (PPD) and 20(S)-Protopanaxatriol (PPT) are major metabolites of ginseng in humans and are considered to have estrogenic activity in cellular bioassays. In this study, we conducted in silico analyses to determine whether PPD and PPT interact with estrogen receptor alpha (ERα) and compared them with ERα agonists, partial agonists, and antagonists to identify their ERα activity. The transcriptome profile of 17β-estradiol (E2), PPD, and PPT in MCF-7 cells expressing ERα was further compared to understand the ERα activity of ginsenoside metabolites. The results showed that PPD and PPT interacted with the 1ERE, 1GWR, and 3UUD ERα proteins in the E2 interaction model, the 3ERD protein in the diethylstilbestrol (DES) interaction model, and the 1X7R protein in the genistein (GEN) interaction model. Conversely, neither the 4PP6 protein of the interaction model with the antagonist resveratrol (RES) nor the 1ERR protein of the interaction model with the antagonist raloxifene (RAL) showed the conformation of amino acid residues. When E2, PPD, and PPT were exposed to MCF-7 cells, cell proliferation and gene expression were observed. The transcriptomic profiles of E2, PPD, and PPT were compared using a knowledge-based pathway. PPD-induced transcription profiling was similar to that of E2, and the neural transmission pathway was detected in both compounds. In contrast, PPT-induced transcription profiling displayed characteristics of gene expression associated with systemic lupus erythematosus. These results suggest that ginsenoside metabolites have ERα agonist activity and exhibit neuroprotective effects and anti-inflammatory actions. However, a meta-analysis using public microarray data showed that the mother compounds GRb1 and GRg1 of PPD and PPT showed metabolic functions in insulin signaling pathways, condensed DNA repair and cell cycle pathways, and immune response and synaptogenesis. These results suggest that the ginsenoside metabolites have potent ERα agonist activity; however, their gene expression profiles may differ from those of E2.
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15
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Lan J, Wu C, Liang W, Shen J, Zhuo Z, Hu L, Ruan L, Zhang P, Ye X, Xu L, Li C, Lin S, Yang C, Wu S, Dong Y, Ren H, Huang H, Gao B, Yao H, Lin T, Chen X, Li C. An Effective Treatment of Perimenopausal Syndrome by Combining Two Traditional Prescriptions of Chinese Botanical Drugs. Front Pharmacol 2021; 12:744409. [PMID: 34759822 PMCID: PMC8573068 DOI: 10.3389/fphar.2021.744409] [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: 07/20/2021] [Accepted: 09/20/2021] [Indexed: 12/04/2022] Open
Abstract
Ethnopharmacological relevance: Two types of traditional Chinese formulas of botanical drugs are prescribed for treating perimenopausal syndrome (PMS), a disorder in middle-aged women during their transition to menopause. One is for treating PMS as kidney deficiency (KD) due to senescence and declining reproductive functions, and the other is for treating it as liver qi stagnation (LQS) in association with stress and anxiety. Despite the time-tested prescriptions, an objective attestation to the effectiveness of the traditional Chinese treatment of PMS is still to be established and the associated molecular mechanism is still to be investigated. Materials and methods: A model for PMS was generated from perimenopausal rats with chronic restraint stress (CRS). The effectiveness of traditional Chinese formulas of botanical drugs and a combination of two of the formulas was evaluated based on 1H NMR plasma metabolomic, as well as behavioral and physiological, indicators. To investigate whether the formulas contained ligands that could compensate for the declining level of estrogen, the primary cause of PMS, the ligand-based NMR technique of saturation transfer difference (STD) was employed to detect possible interacting molecules to estrogen receptors in the decoction. Results: Each prescription of the classical Chinese formula moderately attenuated the metabolomic state of the disease model. The best treatment strategy however was to combine two traditional Chinese formulas, each for a different etiology, to adjust the metabolomic state of the disease model to that of rats at a much younger age. In addition, this attenuation of the metabolomics of the disease model was by neither upregulating the estrogen level nor supplementing an estrogenic compound. Conclusion: Treatment of PMS with a traditional Chinese formula of botanical drugs targeting one of the two causes separately could ameliorate the disorder moderately. However, the best outcome was to treat the two causes simultaneously with a decoction that combined ingredients from two traditional prescriptions. The data also implicated a new paradigm for phytotherapy of PMS as the prescribed decoctions contained no interacting compound to modulate the activity of estrogen receptors, in contrast to the treatment strategy of hormone replacement therapy.
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Affiliation(s)
- Junjie Lan
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Caiming Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Wen'na Liang
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Jianying Shen
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Zewei Zhuo
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Liu Hu
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Luwei Ruan
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Pengheng Zhang
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Xiangrong Ye
- Xiamen Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Xiamen, China
| | - Leqin Xu
- Xiamen Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Xiamen, China
| | - Chengfu Li
- Xiamen Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Xiamen, China
| | - Shengyuan Lin
- First Hospital Affiliated to Fujian University of Medicine, Fuzhou, China
| | - Chuanhui Yang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Siqi Wu
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Yingjun Dong
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Haixia Ren
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Huiying Huang
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Bizhen Gao
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
| | - Hongwei Yao
- Institute of Molecular Enzymology, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Tianwei Lin
- State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-Province Joint Engineering Laboratory of Targeted Drugs From Natural Products, School of Life Sciences, Xiamen University, Cancer Research Center of Xiamen University, Xiamen, China
| | - Xueqin Chen
- Xiamen Hospital of Traditional Chinese Medicine Affiliated to Fujian University of Traditional Chinese Medicine, Xiamen, China.,The First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Candong Li
- Research Base of TCM syndrome, Fujian University of Traditional Chinese Medicine, Fuzhou, China
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Siclari JJ, Gardner KH. Two steps, one ligand: How PPARγ binds small-molecule agonists. Structure 2021; 29:935-936. [PMID: 34478635 DOI: 10.1016/j.str.2021.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this issue of Structure,Shang and Kojetin (2021) present insights into the binding mechanism of artificial agonists to the PPARγ nuclear receptor. These data support a two-step model with induced fit and conformational selection aspects. This mechanism may exist in related receptors, providing new opportunities for drug development.
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Affiliation(s)
- James J Siclari
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Ph.D. Program in Biology, Graduate Center, City University of New York, NY 10016, USA
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center, New York, NY 10031, USA; Department of Chemistry and Biochemistry, City College of New York, NY 10031, USA; Ph.D. Programs in Biology, Biochemistry, and Chemistry, Graduate Center, City University of New York, NY 10016, USA.
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17
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Abstract
Efforts to improve estrogen receptor-α (ER)-targeted therapies in breast cancer have relied upon a single mechanism, with ligands having a single side chain on the ligand core that extends outward to determine antagonism of breast cancer growth. Here, we describe inhibitors with two ER-targeting moieties, one of which uses an alternate structural mechanism to generate full antagonism, freeing the side chain to independently determine other critical properties of the ligands. By combining two molecular targeting approaches into a single ER ligand, we have generated antiestrogens that function through new mechanisms and structural paradigms to achieve antagonism. These dual-mechanism ER inhibitors (DMERIs) cause alternate, noncanonical structural perturbations of the receptor ligand-binding domain (LBD) to antagonize proliferation in ER-positive breast cancer cells and in allele-specific resistance models. Our structural analyses with DMERIs highlight marked differences from current standard-of-care, single-mechanism antiestrogens. These findings uncover an enhanced flexibility of the ER LBD through which it can access nonconsensus conformational modes in response to DMERI binding, broadly and effectively suppressing ER activity.
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18
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Elucidation of Agonist and Antagonist Dynamic Binding Patterns in ER-α by Integration of Molecular Docking, Molecular Dynamics Simulations and Quantum Mechanical Calculations. Int J Mol Sci 2021; 22:ijms22179371. [PMID: 34502280 PMCID: PMC8431471 DOI: 10.3390/ijms22179371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/25/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
Estrogen receptor alpha (ERα) is a ligand-dependent transcriptional factor in the nuclear receptor superfamily. Many structures of ERα bound with agonists and antagonists have been determined. However, the dynamic binding patterns of agonists and antagonists in the binding site of ERα remains unclear. Therefore, we performed molecular docking, molecular dynamics (MD) simulations, and quantum mechanical calculations to elucidate agonist and antagonist dynamic binding patterns in ERα. 17β-estradiol (E2) and 4-hydroxytamoxifen (OHT) were docked in the ligand binding pockets of the agonist and antagonist bound ERα. The best complex conformations from molecular docking were subjected to 100 nanosecond MD simulations. Hierarchical clustering was conducted to group the structures in the trajectory from MD simulations. The representative structure from each cluster was selected to calculate the binding interaction energy value for elucidation of the dynamic binding patterns of agonists and antagonists in the binding site of ERα. The binding interaction energy analysis revealed that OHT binds ERα more tightly in the antagonist conformer, while E2 prefers the agonist conformer. The results may help identify ERα antagonists as drug candidates and facilitate risk assessment of chemicals through ER-mediated responses.
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Wan S, Kumar D, Ilyin V, Al Homsi U, Sher G, Knuth A, Coveney PV. The effect of protein mutations on drug binding suggests ensuing personalised drug selection. Sci Rep 2021; 11:13452. [PMID: 34188094 PMCID: PMC8241852 DOI: 10.1038/s41598-021-92785-w] [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: 01/02/2021] [Accepted: 06/09/2021] [Indexed: 11/08/2022] Open
Abstract
The advent of personalised medicine promises a deeper understanding of mechanisms and therefore therapies. However, the connection between genomic sequences and clinical treatments is often unclear. We studied 50 breast cancer patients belonging to a population-cohort in the state of Qatar. From Sanger sequencing, we identified several new deleterious mutations in the estrogen receptor 1 gene (ESR1). The effect of these mutations on drug treatment in the protein target encoded by ESR1, namely the estrogen receptor, was achieved via rapid and accurate protein-ligand binding affinity interaction studies which were performed for the selected drugs and the natural ligand estrogen. Four nonsynonymous mutations in the ligand-binding domain were subjected to molecular dynamics simulation using absolute and relative binding free energy methods, leading to the ranking of the efficacy of six selected drugs for patients with the mutations. Our study shows that a personalised clinical decision system can be created by integrating an individual patient's genomic data at the molecular level within a computational pipeline which ranks the efficacy of binding of particular drugs to variant proteins.
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Affiliation(s)
- Shunzhou Wan
- Department of Chemistry, Centre for Computational Science, University College London, London, WC1H 0AJ, UK
| | - Deepak Kumar
- Computational Biology, Carnegie Mellon University in Qatar (CMU-Q), Doha, Qatar
| | - Valentin Ilyin
- Computational Biology, Carnegie Mellon University in Qatar (CMU-Q), Doha, Qatar
| | - Ussama Al Homsi
- Hematology and Oncology Department, National Center for Cancer Care & Research, Hamad Medical Corporation, Doha, Qatar
| | - Gulab Sher
- Interim Translational Research Institute, Hamad Medical Corporation, Doha, Qatar
| | - Alexander Knuth
- Hematology and Oncology Department, National Center for Cancer Care & Research, Hamad Medical Corporation, Doha, Qatar
| | - Peter V Coveney
- Department of Chemistry, Centre for Computational Science, University College London, London, WC1H 0AJ, UK.
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20
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Díaz M, Lobo F, Hernández D, Amesty Á, Valdés-Baizabal C, Canerina-Amaro A, Mesa-Herrera F, Soler K, Boto A, Marín R, Estévez-Braun A, Lahoz F. FLTX2: A Novel Tamoxifen Derivative Endowed with Antiestrogenic, Fluorescent, and Photosensitizer Properties. Int J Mol Sci 2021; 22:ijms22105339. [PMID: 34069498 PMCID: PMC8161337 DOI: 10.3390/ijms22105339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 04/28/2021] [Accepted: 05/08/2021] [Indexed: 11/16/2022] Open
Abstract
Tamoxifen is the most widely used selective modulator of estrogen receptors (SERM) and the first strategy as coadjuvant therapy for the treatment of estrogen-receptor (ER) positive breast cancer worldwide. In spite of such success, tamoxifen is not devoid of undesirable effects, the most life-threatening reported so far affecting uterine tissues. Indeed, tamoxifen treatment is discouraged in women under risk of uterine cancers. Recent molecular design efforts have endeavoured the development of tamoxifen derivatives with antiestrogen properties but lacking agonistic uterine tropism. One of this is FLTX2, formed by the covalent binding of tamoxifen as ER binding core, 7-nitrobenzofurazan (NBD) as the florescent dye, and Rose Bengal (RB) as source for reactive oxygen species. Our analyses demonstrate (1) FLTX2 is endowed with similar antiestrogen potency as tamoxifen and its predecessor FLTX1, (2) shows a strong absorption in the blue spectral range, associated to the NBD moiety, which efficiently transfers the excitation energy to RB through intramolecular FRET mechanism, (3) generates superoxide anions in a concentration- and irradiation time-dependent process, and (4) Induces concentration- and time-dependent MCF7 apoptotic cell death. These properties make FLTX2 a very promising candidate to lead a novel generation of SERMs with the endogenous capacity to promote breast tumour cell death in situ by photosensitization.
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Affiliation(s)
- Mario Díaz
- Departamento Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 Tenerife, Spain;
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38200 Tenerife, Spain; (A.B.); (R.M.); (F.L.)
- Correspondence:
| | - Fernando Lobo
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain; (F.L.); (Á.A.); (C.V.-B.)
| | - Dácil Hernández
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico F. Sánchez, 38206 Tenerife, Spain;
| | - Ángel Amesty
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain; (F.L.); (Á.A.); (C.V.-B.)
- Instituto Universitario de Bioorgánica “Antonio González”, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Catalina Valdés-Baizabal
- Programa Agustín de Betancourt, Universidad de la Laguna, 38200 Tenerife, Spain; (F.L.); (Á.A.); (C.V.-B.)
- Departamento Ciencias Médicas Básicas, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Ana Canerina-Amaro
- Departamento Ciencias Médicas Básicas, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Fátima Mesa-Herrera
- Departamento Biología Animal, Edafología y Geología, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Kevin Soler
- Departamento Física, IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Alicia Boto
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38200 Tenerife, Spain; (A.B.); (R.M.); (F.L.)
- Instituto de Productos Naturales y Agrobiología del CSIC, Avda. Astrofísico F. Sánchez, 38206 Tenerife, Spain;
| | - Raquel Marín
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38200 Tenerife, Spain; (A.B.); (R.M.); (F.L.)
- Departamento Ciencias Médicas Básicas, Universidad de La Laguna, 38200 Tenerife, Spain;
| | - Ana Estévez-Braun
- Instituto Universitario de Bioorgánica “Antonio González”, Universidad de La Laguna, 38200 Tenerife, Spain;
- Departamento Química Orgánica, Universidad de La Laguna, 38200 Tenerife, Spain
| | - Fernando Lahoz
- Unidad Asociada ULL-CSIC “Fisiología y Biofísica de la Membrana Celular en Enfermedades Neurodegenerativas y Tumorales”, 38200 Tenerife, Spain; (A.B.); (R.M.); (F.L.)
- Departamento Física, IUdEA, Universidad de La Laguna, 38200 Tenerife, Spain;
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21
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Kriegel M, Wiederanders HJ, Alkhashrom S, Eichler J, Muller YA. A PROSS-designed extensively mutated estrogen receptor α variant displays enhanced thermal stability while retaining native allosteric regulation and structure. Sci Rep 2021; 11:10509. [PMID: 34006920 PMCID: PMC8131754 DOI: 10.1038/s41598-021-89785-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/22/2021] [Indexed: 11/13/2022] Open
Abstract
Protein stability limitations often hamper the exploration of proteins as drug targets. Here, we show that the application of PROSS server algorithms to the ligand-binding domain of human estrogen receptor alpha (hERα) enabled the development of variant ERPRS* that comprises 24 amino acid substitutions and exhibits multiple improved characteristics. The protein displays enhanced production rates in E. coli, crystallizes readily and its thermal stability is increased significantly by 23 °C. hERα is a nuclear receptor (NR) family member. In NRs, protein function is allosterically regulated by its interplay with small molecule effectors and the interaction with coregulatory proteins. The in-depth characterization of ERPRS* shows that these cooperative effects are fully preserved despite that 10% of all residues were substituted. Crystal structures reveal several salient features, i.e. the introduction of a tyrosine corner in a helix-loop-helix segment and the formation of a novel surface salt bridge network possibly explaining the enhanced thermal stability. ERPRS* shows that prior successes in computational approaches for stabilizing proteins can be extended to proteins with complex allosteric regulatory behaviors as present in NRs. Since NRs including hERα are implicated in multiple diseases, our ERPRS* variant shows significant promise for facilitating the development of novel hERα modulators.
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Affiliation(s)
- Mark Kriegel
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Hanna J Wiederanders
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Sewar Alkhashrom
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jutta Eichler
- Department of Chemistry and Pharmacy, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Yves A Muller
- Division of Biotechnology, Department of Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Erlangen, Germany.
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22
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Shang J, Kojetin DJ. Structural mechanism underlying ligand binding and activation of PPARγ. Structure 2021; 29:940-950.e4. [PMID: 33713599 DOI: 10.1016/j.str.2021.02.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 12/16/2022]
Abstract
Ligands bind to an occluded orthosteric ligand-binding pocket within the nuclear receptor ligand-binding domain. Molecular simulations have revealed theoretical ligand entry/exit pathways to the orthosteric pocket; however, it remains unclear whether ligand binding proceeds through induced fit or conformational selection mechanisms. Here, using nuclear magnetic resonance spectroscopy, isothermal titration calorimetry, and surface plasmon resonance analysis, we provide evidence that structurally distinct agonists bind peroxisome proliferator-activated receptor γ (PPARγ) via a two-step induced fit mechanism involving an initial fast kinetic step followed by a slow conformational change. The agonist encounter complex binding pose is suggested in crystal structures where ligands bind to a surface pore suggested as a ligand entry site in molecular simulations. Our findings suggest an activation mechanism for PPARγ whereby agonist binding occurs through an initial encounter complex followed by a transition of the ligand into the final binding pose within the orthosteric pocket, inducing a transcriptionally active conformation.
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Affiliation(s)
- Jinsai Shang
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Douglas J Kojetin
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL 33458, USA; Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL 33458, USA.
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23
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Shylaja R, Loganathan C, Kabilan S, Vijayakumar T, Meganathan C. Synthesis and evaluation of the antagonistic activity of 3-acetyl-2H-benzo[g]chromen-2-one against mutant Y537S estrogen receptor alpha via E-Pharmacophore modeling, molecular docking, molecular dynamics, and in-vitro cytotoxicity studies. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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24
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Tan H, Wang X, Hong H, Benfenati E, Giesy JP, Gini GC, Kusko R, Zhang X, Yu H, Shi W. Structures of Endocrine-Disrupting Chemicals Determine Binding to and Activation of the Estrogen Receptor α and Androgen Receptor. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:11424-11433. [PMID: 32786601 DOI: 10.1021/acs.est.0c02639] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Endocrine-disrupting chemicals (EDCs) can interact with nuclear receptors, including estrogen receptor α (ERα) and androgen receptor (AR), to affect the normal endocrine system function, causing severe symptoms. Limited studies queried the EDC mechanisms, focusing on limited chemicals or a set of structurally similar compounds. It remained uncertain how hundreds of diverse EDCs could bind to ERα and AR and cause distinct functional consequences. Here, we employed a series of computational methodologies to investigate the structural features of EDCs that bind to and activate ERα and AR based on more than 4000 compounds. We used molecular docking and molecular dynamics simulations to elucidate the functional consequences and validated structure-function correlations experimentally using a time-resolved fluorescence resonance energy-transfer assay. We found that EDCs share three levels of key fragments. Primary (20 for ERα and 18 for AR) and secondary fragments (38 for ERα and 29 for AR) are responsible for the binding to receptors, and tertiary fragments determine the activity type (agonist, antagonist, or mixed). In summary, our study provides a general mechanism for the EDC function. Discovering the three levels of key fragments may drive fast screening and evaluation of potential EDCs from large sets of commercially used synthetic compounds.
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Affiliation(s)
- Haoyue Tan
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Xiaoxiang Wang
- State Environmental Protection Key Laboratory of Integrated Surface Water-Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Huixiao Hong
- National Center for Toxicological Research US Food and Drug Administration, 3900 NCTR Rd., Jefferson 72079, Arkansas, United States
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via G. La Masa 19, Milan 20156, Italy
| | - John P Giesy
- Toxicology Centre, University of Saskatchewan, Saskatoon S7N 5B3, Canada
- Department of Veterinary Biomedical Sciences, University of Saskatchewan, Saskatoon S7N 5B4, Canada
- Department of Environmental Sciences, Baylor University, Waco 76706, Texas, United States
| | - Giuseppina C Gini
- Department of Electronics and Information, Politecnico di Milano, Piazza L. da Vinci 32, Milano 20133, Italy
| | - Rebeca Kusko
- Immuneering Corporation, Cambridge 02142, Massachusetts, United States
| | - Xiaowei Zhang
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Hongxia Yu
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
| | - Wei Shi
- State Key Laboratory of Pollution Control and Resources Reuse, School of the Environment, Nanjing University, Nanjing 210023, Jiangsu, China
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25
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Anananuchatkul T, Chang IV, Miki T, Tsutsumi H, Mihara H. Construction of a Stapled α-Helix Peptide Library Displayed on Phage for the Screening of Galectin-3-Binding Peptide Ligands. ACS OMEGA 2020; 5:5666-5674. [PMID: 32226843 PMCID: PMC7097893 DOI: 10.1021/acsomega.9b03461] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 02/24/2020] [Indexed: 06/10/2023]
Abstract
A stapled α-helix peptide library was designed and constructed using a chemically modified phage display system for screening stapled-peptide ligands against target proteins. The α-helix peptide library, with two cysteine residues on the opposite side of the randomized face, was modified with a rigid hydrocarbon staple linker on a phage. The stapled α-helix peptide phage library was screened against galectin-3 (Gal-3), a cancer-related galactose-binding protein. The obtained stapled peptides showed a high binding affinity (K d = 0.45 μM) despite being nonsugar ligands. The stapled modification played important roles in stabilizing the α-helical structure that contributed to the high binding affinity to Gal-3. In addition, the best stapled peptide ligands showed specific binding to Gal-3 among various carbohydrate-binding proteins. Thus, the designed α-helix peptide phage library with a constrained structure by the staple linker will advance the discovery of peptide ligands with improved specificity and affinity.
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26
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Chinnasamy K, Saravanan M, Poomani K. Investigation of binding mechanism and downregulation of elacestrant for wild and L536S mutant estrogen receptor-α through molecular dynamics simulation and binding free energy analysis. J Comput Chem 2020; 41:97-109. [PMID: 31602686 DOI: 10.1002/jcc.26076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 06/22/2019] [Accepted: 08/31/2019] [Indexed: 12/11/2022]
Abstract
The selective estrogen receptor downregulators (SERDs) are the new emerging class of drugs that are used for the treatment of endocrine resistance breast cancer. Elacestrant (ELA) is a new SERD, currently it is in phase II clinical trial. To understand the ELA-ERα interactions, the molecular docking analysis has been carried out. The ELA molecule binds with the helices H3, H5, H6, and H11 and forms important intermolecular interactions. In addition to this, the tetrahydronapthalene and phenyl rings of ELA are forming T-shaped π···π interactions with the Phe404 and Trp383 residues. Further to understand the stability and flexibility of ELA molecule in the active site of wild and mutated L536S ERα, 100ns molecular dynamics (MD) simulation was performed for both complexes. Interestingly, the MD analysis of wild complex revealed an interaction between ELA and the Asn532 of H11, which is an essential interaction for the downregulation/degradation of ERα, whereas this interaction is not observed in the mutated complex. The drug binding mechanism and H12 dynamics have been elucidated from the analysis of hydrogen bonding interactions and the secondary structure analysis. To explore the binding affinity of ELA molecule, the binding free energy and normal mode analyses were carried out. The per residue decomposition analysis also performed, which shows the contribution of individual amino acids. The principal component analysis and residue interaction network analysis were used to identify the modifications and the interaction between the residues. From the results of different analysis, the inhibition mechanism and downregulation of ERα-ELA complex has been investigated. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Kalaiarasi Chinnasamy
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Manjula Saravanan
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
| | - Kumaradhas Poomani
- Laboratory of Biocrystallography and Computational molecular Biology, Department of Physics, Periyar University, Salem, 636 011, India
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27
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Jiang W, Chen Q, Zhou B, Wang F. In silico prediction of estrogen receptor subtype binding affinity and selectivity using 3D-QSAR and molecular docking. Med Chem Res 2019. [DOI: 10.1007/s00044-019-02428-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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28
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Marcovitz A, Turakhia Y, Chen HI, Gloudemans M, Braun BA, Wang H, Bejerano G. A functional enrichment test for molecular convergent evolution finds a clear protein-coding signal in echolocating bats and whales. Proc Natl Acad Sci U S A 2019; 116:21094-21103. [PMID: 31570615 PMCID: PMC6800341 DOI: 10.1073/pnas.1818532116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Distantly related species entering similar biological niches often adapt by evolving similar morphological and physiological characters. How much genomic molecular convergence (particularly of highly constrained coding sequence) contributes to convergent phenotypic evolution, such as echolocation in bats and whales, is a long-standing fundamental question. Like others, we find that convergent amino acid substitutions are not more abundant in echolocating mammals compared to their outgroups. However, we also ask a more informative question about the genomic distribution of convergent substitutions by devising a test to determine which, if any, of more than 4,000 tissue-affecting gene sets is most statistically enriched with convergent substitutions. We find that the gene set most overrepresented (q-value = 2.2e-3) with convergent substitutions in echolocators, affecting 18 genes, regulates development of the cochlear ganglion, a structure with empirically supported relevance to echolocation. Conversely, when comparing to nonecholocating outgroups, no significant gene set enrichment exists. For aquatic and high-altitude mammals, our analysis highlights 15 and 16 genes from the gene sets most affected by molecular convergence which regulate skin and lung physiology, respectively. Importantly, our test requires that the most convergence-enriched set cannot also be enriched for divergent substitutions, such as in the pattern produced by inactivated vision genes in subterranean mammals. Showing a clear role for adaptive protein-coding molecular convergence, we discover nearly 2,600 convergent positions, highlight 77 of them in 3 organs, and provide code to investigate other clades across the tree of life.
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Affiliation(s)
- Amir Marcovitz
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | - Yatish Turakhia
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305
| | - Heidi I Chen
- Department of Developmental Biology, Stanford University, Stanford, CA 94305
| | | | - Benjamin A Braun
- Department of Computer Science, Stanford University, Stanford, CA 94305
| | - Haoqing Wang
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305
| | - Gill Bejerano
- Department of Developmental Biology, Stanford University, Stanford, CA 94305;
- Department of Computer Science, Stanford University, Stanford, CA 94305
- Department of Pediatrics, Stanford University, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305
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29
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Ge J, Remesh SG, Hammel M, Pan S, Mahan AD, Wang S, Wang X. Functional Relevance of Interleukin-1 Receptor Inter-domain Flexibility for Cytokine Binding and Signaling. Structure 2019; 27:1296-1307.e5. [PMID: 31257107 DOI: 10.1016/j.str.2019.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Revised: 04/09/2019] [Accepted: 05/24/2019] [Indexed: 02/08/2023]
Abstract
The interleukin 1 (IL-1) receptor family, whose members contain three immunoglobulin-like domains (D1-D3) in the extracellular region, is responsible for transmitting pleiotropic signals of IL-1 cytokines. The inter-domain flexibility of IL-1 receptors and its functional roles have not been fully elucidated. In this study, we used small-angle X-ray scattering to show that ligand-binding primary receptors and co-receptors in the family all have inherent inter-domain flexibility due to the D2/D3 linker. Variants of the IL-1RAcP and IL-18Rβ co-receptors with mutated D2/D3 linkers cannot form a cytokine-receptor complex and mediate signaling. Our analysis further revealed that these mutated co-receptors exhibited a changed conformational ensemble, suggesting that loss of function is due to the alteration of receptor dynamics. Taken together, our results demonstrate that the D2/D3 linker is a critical functional determinant of IL-1 receptor and underscore the important roles of the inter-domain flexibility in cytokine/receptor binding and signaling.
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Affiliation(s)
- Jiwan Ge
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Soumya G Remesh
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Si Pan
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Andrew D Mahan
- Janssen Bio Therapeutics, Janssen R&D, LLC, Spring House, PA 19477, USA
| | - Shuying Wang
- Department of Microbiology and Immunology, National Cheng Kung University Medical College, Tainan 701, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan 701, Taiwan.
| | - Xinquan Wang
- Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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30
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Determination and analysis of agonist and antagonist potential of naturally occurring flavonoids for estrogen receptor (ERα) by various parameters and molecular modelling approach. Sci Rep 2019; 9:7450. [PMID: 31092862 PMCID: PMC6520524 DOI: 10.1038/s41598-019-43768-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 04/17/2019] [Indexed: 12/29/2022] Open
Abstract
Most estrogen receptor α (ERα) ligands target the ligand binding domain (LBD). Agonist 17β-estradiol (E2) and tamoxifen (TM, known SERM), bind to the same site within the LBD. However, structures of ligand-bound complexes show that E2 and TM induce different conformations of helix 12 (H12). During the molecular modelling studies of some naturally occurring flavonoids such as quercetin, luteolin, myricetin, kaempferol, naringin, hesperidin, galangin, baicalein and epicatechin with human ERα (3ERT and 1GWR), we observed that most of the ligands bound to the active site pocket of both 3ERT and 1GWR. The docking scores, interaction analyses, and conformation of H12 provided the data to support for the estrogenic or antiestrogenic potential of these flavonoids to a limited degree. Explicit molecular dynamics for 50 ns was performed to identify the stability and compatibility pattern of protein-ligand complex and RMSD were obtained. Baicalein, epicatechin, and kaempferol with 1GWR complex showed similar RMSD trend with minor deviations in the protein backbone RMSD against 1GWR-E2 complex that provided clear indications that ligands were stable throughout the explicit molecular simulations in the protein and outcome of naringin-3ERT complex had an upward trend but stable throughout the simulations and all molecular dynamics showed stability with less than overall 1 Å deviation throughout the simulations. To examine their estrogenic or antiestrogenic potential, we studied the effect of the flavonoids on viability, progesterone receptor expression and 3xERE/3XERRE-driven reporter gene expression in ERα positive and estrogen responsive MCF-7 breast cancer cells. Epicatechin, myricetin, and kaempferol showed estrogenic potential at 5 µM concentration.
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31
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TilakVijay J, Vivek Babu K, Uma A. Virtual screening of novel compounds as potential ER-alpha inhibitors. Bioinformation 2019; 15:321-332. [PMID: 31249434 PMCID: PMC6589477 DOI: 10.6026/97320630015321] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 04/12/2019] [Indexed: 12/25/2022] Open
Abstract
Majority of breast cancers diagnosed today are estrogen receptor (ER)-positive, however, progesterone receptor-positive (PR-positive) is also responsible for breast cancer. Tumors that are ER/PR-positive are much more likely to respond to hormone therapy than tumors that are ER/PR-negative. Nearly 105 ERa inhibitors from literature when docked resulted in 31 compounds (pyrazolo[1,5-a]pyrimidine analogs and chromen-2-one derivatives) with better binding affinities. The maximum score obtained was -175.282 kcal/mol for compound, [2-(4- Fluoro-phenylamino)-pyridin-3-yl]-{4-[2-phenyl-7- (3, 4, 5-trimethoxy-phenyl)-pyrazolo[1,5-a]pyrimidine-5-carbonyl]-piperazin-1-yl}-methanone. The major H-bond interactions are observed with Thr347. In pursuit to identify novel ERa inhibitory ligands, virtual screening was carried out by docking pyrazole, bipyrazole, thiazole, thiadiazole etc scaffold analogs from literature.34 bipyrazoles from literature revealed Compound 2, ethyl 5-amino-1-(5-amino-3-anilino-4-ethoxycarbonyl-pyrazol-1-yl)-3-anilino-pyrazole-4-carboxylate, with -175.9 kcal/mol binding affinity with the receptor, where a favourable H-bond was formed with Thr347.On the other hand, screening 2035 FDA approved drugs from Drug Bank database resulted in 11 drugs which showed better binding affinities than ERa bound tamoxifen. Consensus scoring using 5 scoring schemes such as Mol Dock score, mcule, SwissDock, Pose&Rank and DSX respectively resulted in better rank-sumsfor Lomitapide, Itraconazole, Cobicistat, Azilsartanmedoxomil, and Zafirlukast.
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Affiliation(s)
- Jakkanaboina TilakVijay
- Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University, Hyderabad, Telungana, India
| | - Kandimalla Vivek Babu
- Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University, Hyderabad, Telungana, India
| | - Addepally Uma
- Centre for Biotechnology, Institute of Science and Technology, Jawaharlal Nehru Technological University, Hyderabad, Telungana, India
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32
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Cao H, Wang L, Liang Y, Li Z, Feng H, Sun Y, Zhang A, Fu J. Protonation state effects of estrogen receptor α on the recognition mechanisms by perfluorooctanoic acid and perfluorooctane sulfonate: A computational study. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 171:647-656. [PMID: 30658300 DOI: 10.1016/j.ecoenv.2019.01.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 12/20/2018] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
Perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) have been reported to cause adverse health effects on wildlife as well as humans. Numerous studies demonstrated that PFOA and PFOS could interfere with the transcriptional activation of estrogen receptor α (ERα) by mimicking the function of endogenous ligand, whereas some reports suggested that the two compounds present non-estrogenic activities. These conflicting results bring a confusion to understand their molecular mechanism on the ERα-mediated signaling pathway. To address this issue, we performed the molecular docking and molecular dynamics simulations to elaborate the structural characteristics for the binding of PFOA and PFOS to ERα. Our results indicated that the two opposite binding orientations were modulated by the protonation states of key residue His524. In sub-acidic condition, PFOA and PFOS prefer to form the H-bonding interactions with the protonated His524, whereas Arg394 provided the H-bonding interactions for stable binding in sub-alkaline condition. Conformational analyses implied that the diverse binding modes were closely related to the conformational propensity of ERα for subsequent coactivator recruitment and transcription activation. Generally, our findings provide a flexible strategy to assess the pH impacts of microenvironment on the toxicities of perfluoroalkyl acids by their interactions with proteins.
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Affiliation(s)
- Huiming Cao
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Ling Wang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Yong Liang
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Zhunjie Li
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Hongru Feng
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China
| | - Yuzhen Sun
- Institute of Environment and Health, Jianghan University, Wuhan 430056, China
| | - Aiqian Zhang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China; Institute of Environment and Health, Jianghan University, Wuhan 430056, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100190, China.
| | - Jianjie Fu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Science, Beijing 100085, China.
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33
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Spiriti J, Subramanian SR, Palli R, Wu M, Zuckerman DM. Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α. PLoS One 2019; 14:e0215694. [PMID: 31013302 PMCID: PMC6478315 DOI: 10.1371/journal.pone.0215694] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/06/2019] [Indexed: 12/17/2022] Open
Abstract
There is a vast gulf between the two primary strategies for simulating protein-ligand interactions. Docking methods significantly limit or eliminate protein flexibility to gain great speed at the price of uncontrolled inaccuracy, whereas fully flexible atomistic molecular dynamics simulations are expensive and often suffer from limited sampling. We have developed a flexible docking approach geared especially for highly flexible or poorly resolved targets based on mixed-resolution Monte Carlo (MRMC), which is intended to offer a balance among speed, protein flexibility, and sampling power. The binding region of the protein is treated with a standard atomistic force field, while the remainder of the protein is modeled at the residue level with a Gō model that permits protein flexibility while saving computational cost. Implicit solvation is used. Here we assess three facets of the MRMC approach with implications for other docking studies: (i) the role of receptor flexibility in cross-docking pose prediction; (ii) the use of non-equilibrium candidate Monte Carlo (NCMC) and (iii) the use of pose-clustering in scoring. We examine 61 co-crystallized ligands of estrogen receptor α, an important cancer target known for its flexibility. We also compare the performance of the MRMC approach with Autodock smina. Adding protein flexibility, not surprisingly, leads to significantly lower total energies and stronger interactions between protein and ligand, but notably we document the important role of backbone flexibility in the improvement. The improved backbone flexibility also leads to improved performance relative to smina. Somewhat unexpectedly, our implementation of NCMC leads to only modestly improved sampling of ligand poses. Overall, the addition of protein flexibility improves the performance of docking, as measured by energy-ranked poses, but we do not find significant improvements based on cluster information or the use of NCMC. We discuss possible improvements for the model including alternative coarse-grained force fields, improvements to the treatment of solvation, and adding additional types of NCMC moves.
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Affiliation(s)
- Justin Spiriti
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
| | - Sundar Raman Subramanian
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Rohith Palli
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Maria Wu
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Daniel M. Zuckerman
- Department of Biomedical Engineering, Oregon Health and Science University, Portland, OR 97239, United States of America
- * E-mail:
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Okafor CD, Colucci JK, Ortlund EA. Ligand-Induced Allosteric Effects Governing SR Signaling. NUCLEAR RECEPTOR RESEARCH 2019. [DOI: 10.32527/2019/101382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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He M, Luo P, Hong J, Wang X, Wu H, Zhang R, Qu F, Xiang Y, Xu W. Structural Analysis of Biomolecules through a Combination of Mobility Capillary Electrophoresis and Mass Spectrometry. ACS OMEGA 2019; 4:2377-2386. [PMID: 31459477 PMCID: PMC6648644 DOI: 10.1021/acsomega.8b03224] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 01/24/2019] [Indexed: 05/08/2023]
Abstract
The 3D structures of biomolecules determine their biological function. Established methods in biomolecule structure determination typically require purification, crystallization, or modification of target molecules, which limits their applications for analyzing trace amounts of biomolecules in complex matrices. Here, we developed instruments and methods of mobility capillary electrophoresis (MCE) and its coupling with MS for the 3D structural analysis of biomolecules in the liquid phase. Biomolecules in complex matrices could be separated by MCE and sequentially detected by MS. The effective radius and the aspect ratio of each separated biomolecule were simultaneously determined through the separation by MCE, which were then used as restraints in determining biomolecule conformations through modeling. Feasibility of this method was verified by analyzing a mixture of somatostatin and bradykinin, two peptides with known liquid-phase structures. Proteins could also be structurally analyzed using this method, which was demonstrated for lysozyme. The combination of MCE and MS for complex sample analysis was also demonstrated. MCE and MCE-MS would allow us to analyze trace amounts of biomolecules in complex matrices, which has the potential to be an alternative and powerful biomolecule structure analysis technique.
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Affiliation(s)
- Muyi He
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Pan Luo
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Jie Hong
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Xiaofeng Wang
- Institute
of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Haimei Wu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Rongkai Zhang
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Feng Qu
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
| | - Ye Xiang
- Beijing
Advanced Innovation Center for Structural Biology, Department of Basic
Medical Sciences, School of Medicine, Tsinghua
University, Beijing 100084, China
- E-mail: (Y.X.)
| | - Wei Xu
- College
of Information Science, Shenzhen University, Shenzhen 518060, China
- School
of Life Science, Beijing Institute of Technology, Beijing 100081, China
- E-mail: (W.X.)
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Oguro H. The Roles of Cholesterol and Its Metabolites in Normal and Malignant Hematopoiesis. Front Endocrinol (Lausanne) 2019; 10:204. [PMID: 31001203 PMCID: PMC6454151 DOI: 10.3389/fendo.2019.00204] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 03/12/2019] [Indexed: 12/20/2022] Open
Abstract
Hematopoiesis is sustained throughout life by hematopoietic stem cells (HSCs) that are capable of self-renewal and differentiation into hematopoietic progenitor cells (HPCs). There is accumulating evidence that cholesterol homeostasis is an important factor in the regulation of hematopoiesis. Increased cholesterol levels are known to promote proliferation and mobilization of HSCs, while hypercholesterolemia is associated with expansion of myeloid cells in the peripheral blood and links hematopoiesis with cardiovascular disease. Cholesterol is a precursor to steroid hormones, oxysterols, and bile acids. Among steroid hormones, 17β-estradiol (E2) induces HSC division and E2-estrogen receptor α (ERα) signaling causes sexual dimorphism of HSC division rate. Oxysterols are oxygenated derivatives of cholesterol and key substrates for bile acid synthesis and are considered to be bioactive lipids, and recent studies have begun to reveal their important roles in the hematopoietic and immune systems. 27-Hydroxycholesterol (27HC) acts as an endogenous selective estrogen receptor modulator and induces ERα-dependent HSC mobilization and extramedullary hematopoiesis. 7α,25-dihydroxycholesterol (7α,25HC) acts as a ligand for Epstein-Barr virus-induced gene 2 (EBI2) and directs migration of B cells in the spleen during the adaptive immune response. Bile acids serve as chemical chaperones and alleviate endoplasmic reticulum stress in HSCs. Cholesterol metabolism is dysregulated in hematologic malignancies, and statins, which inhibit de novo cholesterol synthesis, have cytotoxic effects in malignant hematopoietic cells. In this review, recent advances in our understanding of the roles of cholesterol and its metabolites as signaling molecules in the regulation of hematopoiesis and hematologic malignancies are summarized.
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Massafra V, Pellicciari R, Gioiello A, van Mil SW. Progress and challenges of selective Farnesoid X Receptor modulation. Pharmacol Ther 2018; 191:162-177. [DOI: 10.1016/j.pharmthera.2018.06.009] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Wang N, Zou Q, Xu J, Zhang J, Liu J. Ligand binding and heterodimerization with retinoid X receptor α (RXRα) induce farnesoid X receptor (FXR) conformational changes affecting coactivator binding. J Biol Chem 2018; 293:18180-18191. [PMID: 30275017 DOI: 10.1074/jbc.ra118.004652] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/27/2018] [Indexed: 12/29/2022] Open
Abstract
Nuclear receptor farnesoid X receptor (FXR) functions as the major bile acid sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. Because of its central role in metabolism, FXR represents an important drug target to manage metabolic and other diseases, such as primary biliary cirrhosis and nonalcoholic steatohepatitis. FXR and nuclear receptor retinoid X receptor α (RXRα) form a heterodimer that controls the expression of numerous downstream genes. To date, the structural basis and functional consequences of the FXR/RXR heterodimer interaction have remained unclear. Herein, we present the crystal structures of the heterodimeric complex formed between the ligand-binding domains of human FXR and RXRα. We show that both FXR and RXR bind to the transcriptional coregulator steroid receptor coactivator 1 with higher affinity when they are part of the heterodimer complex than when they are in their respective monomeric states. Furthermore, structural comparisons of the FXR/RXRα heterodimers and the FXR monomers bound with different ligands indicated that both heterodimerization and ligand binding induce conformational changes in the C terminus of helix 11 in FXR that affect the stability of the coactivator binding surface and the coactivator binding in FXR. In summary, our findings shed light on the allosteric signal transduction in the FXR/RXR heterodimer, which may be utilized for future drug development targeting FXR.
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Affiliation(s)
- Na Wang
- From the School of Life Sciences, University of Science and Technology of China, Hefei 230026, China,; the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and
| | - Qingan Zou
- Guangzhou Henovcom Biosciences Inc., Guangzhou 510530, China
| | - Jinxin Xu
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and
| | - Jiancun Zhang
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and; Guangzhou Henovcom Biosciences Inc., Guangzhou 510530, China
| | - Jinsong Liu
- the State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China,; the Guangdong Provincial Key Laboratory of Biocomputing, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China, and.
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Weiß RG, Chudoba R, Setny P, Dzubiella J. Affinity, kinetics, and pathways of anisotropic ligands binding to hydrophobic model pockets. J Chem Phys 2018; 149:094902. [DOI: 10.1063/1.5025118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Affiliation(s)
- R. Gregor Weiß
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Laboratory of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Richard Chudoba
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Research Group Simulations of Energy Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany
| | - Piotr Setny
- Centre of New Technologies, University of Warsaw, Stefana Banacha 2c, 00-927 Warsaw, Poland
| | - Joachim Dzubiella
- Institut für Physik, Humboldt-Universität zu Berlin, Newtonstraße 15, D-12489 Berlin, Germany
- Research Group Simulations of Energy Materials, Helmholtz-Zentrum Berlin, Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
- Physikalisches Institut, Albert-Ludwigs-Universität Freiburg, Hermann-Herder Straße 3, D-79104 Freiburg, Germany
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Wiedemann B, Weisner J, Rauh D. Chemical modulation of transcription factors. MEDCHEMCOMM 2018; 9:1249-1272. [PMID: 30151079 PMCID: PMC6097187 DOI: 10.1039/c8md00273h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/10/2018] [Indexed: 12/12/2022]
Abstract
Transcription factors (TFs) constitute a diverse class of sequence-specific DNA-binding proteins, which are key to the modulation of gene expression. TFs have been associated with human diseases, including cancer, Alzheimer's and other neurodegenerative diseases, which makes this class of proteins attractive targets for chemical biology and medicinal chemistry research. Since TFs lack a common binding site or structural similarity, the development of small molecules to efficiently modulate TF biology in cells and in vivo is a challenging task. This review highlights various strategies that are currently being explored for the identification and development of modulators of Myc, p53, Stat, Nrf2, CREB, ER, AR, HIF, NF-κB, and BET proteins.
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Affiliation(s)
- Bianca Wiedemann
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
| | - Jörn Weisner
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
| | - Daniel Rauh
- Technische Universität Dortmund , Fakultät für Chemie und Chemische Biologie , Otto-Hahn-Strasse 4a , D-44227 Dortmund , Germany . ; ; Tel: +49 (0)231 755 7080
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Hou TY, Weng CF, Leong MK. Insight Analysis of Promiscuous Estrogen Receptor α-Ligand Binding by a Novel Machine Learning Scheme. Chem Res Toxicol 2018; 31:799-813. [PMID: 30019586 DOI: 10.1021/acs.chemrestox.8b00130] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Estrogen receptor α (ERα) plays a significant role in occurrence of breast cancer and may cause various adverse side-effects when ERα is an off-target protein. A theoretical model was derived to predict the binding affinity of ERα using the pharmacophore ensemble/support vector machine (PhE/SVM) scheme to consider the promiscuous characteristic of ERα. The estimations by PhE/SVM were discovered to be in good agreement with the observed values for those training molecules ( n = 31, r2 = 0.80, qCV2 = 0.77, RMSE = 0.57, s = 0.58), test molecules ( n = 179, q2 = 0.91-0.96, RMSE = 0.33, s = 0.26) and outliers ( n = 15, q2 = 0.80-0.86, RMSE = 0.56, s = 0.49). When subjected to various statistical validations, the PhE/SVM model consistently fulfilled the strictest criteria. A mock test also asserted its predictivity. When compared with crystal structures, the calculated results are consistent with the reported ERα-ligand co-complex structure, and the plasticity nature of ERα is also disclosed. Consequently, this precise, fast, and robust model can be adopted to predict ERα-ligand binding affinities and to design safer non-ERα-targeted pharmaceuticals in the process of drug discovery and development.
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42
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Zhang J, Wu W, Wang Y, Xing X, Zhong S, Guan T, Zhang T, Hou L, Li T. Estrogen receptor-based fluorescence polarization assay for bisphenol analogues and molecular modeling study of their complexation mechanism. Anal Chim Acta 2018; 1032:107-113. [PMID: 30143207 DOI: 10.1016/j.aca.2018.05.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 04/17/2018] [Accepted: 05/10/2018] [Indexed: 02/03/2023]
Abstract
A fluorescence polarization (FP) assay based on estrogen receptor was developed for the determination of bisphenol compounds (BPs). The human estrogen receptor α ligand binding domain (hERα-LBD) and coumestrol were employed as recognition element and fluorescent probe, respectively. Competitive displacement of tracer from receptor suggested that BPs exhibited dose-dependent binding to hERα-LBD. In order to elucidate the structural basis for the interaction between BPs and hERα-LBD, molecular dynamics simulations were performed to explore their complexation mechanism. The docked bisphenol compounds adopted agonist/antagonist conformations with varying positions and orientations in the hydrophobic binding pocket, depending on their structural characteristics of bridging moieties. Interestingly, the calculated binding energies were generally correlated with the experimentally measured affinities, indicating a potential advantage of the molecular modeling approach in predicting the binding potencies of putative ligands. Considering that the real samples may contain more than one BP, the established FP assay can potentially be used as a pre-screening method to determine the total amounts of bisphenol compounds.
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Affiliation(s)
- Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Wenfu Wu
- College of Biological and Agricultural Engineering, Jilin University, Changchun, 130022, China
| | - Yongjun Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - XiaoJia Xing
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Shuning Zhong
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tianzhu Guan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
| | - Ligang Hou
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Tiezhu Li
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
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43
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Phytoestrogenic Activity of Blackcurrant Anthocyanins Is Partially Mediated through Estrogen Receptor Beta. Molecules 2017; 23:molecules23010074. [PMID: 29286333 PMCID: PMC6017224 DOI: 10.3390/molecules23010074] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 01/09/2023] Open
Abstract
Phytoestrogens are plant compounds with estrogenic effects found in many foods. We have previously reported phytoestrogen activity of blackcurrant anthocyanins (cyanidin-3-glucoside, cyanidin-3-rutinoside, delphinidin-3-glucoside, and delphinidin-3-rutinoside) via the estrogen receptor (ER)α. In this study, we investigated the participation of ERβ in the phytoestrogen activity of these anthocyanins. Blackcurrant anthocyanin induced ERβ-mediated transcriptional activity, and the IC50 of ERβ was lower than that of ERα, indicating that blackcurrant anthocyanins have a higher binding affinity to ERβ. In silico docking analysis of cyanidin and delphinidin, the core portions of the compound that fits within the ligand-binding pocket of ERβ, showed that similarly to 17β-estradiol, hydrogen bonds formed with the ERβ residues Glu305, Arg346, and His475. No fitting placement of glucoside or rutinoside sugar chains within the ligand-binding pocket of ERβ-estradiol complex was detected. However, as the conformation of helices 3 and 12 in ERβ varies depending on the ligand, we suggest that the surrounding structure, including these helices, adopts a conformation capable of accommodating glucoside or rutinoside. Comparison of ERα and ERβ docking structures revealed that the selectivity for ERβ is higher than that for ERα, similar to genistein. These results show that blackcurrant anthocyanins exert phytoestrogen activity via ERβ.
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44
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Zhang J, Li T, Wang T, Yuan C, Zhong S, Guan T, Li Z, Wang Y, Yu H, Luo Q, Wang Y, Zhang T. Estrogenicity of halogenated bisphenol A: in vitro and in silico investigations. Arch Toxicol 2017; 92:1215-1223. [PMID: 29152682 DOI: 10.1007/s00204-017-2127-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/15/2017] [Indexed: 12/23/2022]
Abstract
The binding interactions of bisphenol A (BPA) and its halogenated derivatives (halogenated BPAs) to human estrogen receptor α ligand binding domain (hERα-LBD) was investigated using a combined in vitro and in silico approach. First, the recombinant hERα-LBD was prepared as a soluble protein in Escherichia coli BL21(DE3)pLysS. A native fluorescent phytoestrogen, coumestrol, was employed as tracer for the fluorescence polarization assay. The results of the in vitro binding assay showed that bisphenol compounds could bind to hERα-LBD as the affinity ligands. All the tested halogenated BPAs exhibited weaker receptor binding than BPA, which might be explained by the steric effect of substituents. Molecular docking studies elucidated that the halogenated BPAs adopted different conformations in the flexible hydrophobic ligand binding pocket (LBP), which is mainly dependent on their distinct halogenation patterns. The compounds with halogen substituents on the phenolic rings and on the bridging alkyl moiety acted as agonists and antagonists for hERα, respectively. Interestingly, all the compounds in the agonist conformation of hERα formed a hydrogen bond with His524, while the compounds in the antagonist conformation formed a hydrogen bond with Thr347. These docking results suggested a pivotal role of His524/Thr347 in maintaining the hERα structure in the biologically active agonist/antagonist conformation. Comparison of the calculated binding energies vs. experimental binding affinities yielded a good correlation, which might be applicable for the structure-based design of novel bisphenol compounds with reduced toxicities and for environmental risk assessment. In addition, based on hERα-LBD as a recognition element, the proposed fluorescence polarization assay may offer an alternative to chromatographic techniques for the multi-residue determination of bisphenol compounds.
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Affiliation(s)
- Jie Zhang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Tiezhu Li
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Tuoyi Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Cuiping Yuan
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Shuning Zhong
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tianzhu Guan
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Zhuolin Li
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Yongzhi Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Hansong Yu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, 130118, China
| | - Quan Luo
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun, 130012, China
| | - Yongjun Wang
- Institute of Agricultural Resources and Environment, Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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Oguro H, McDonald JG, Zhao Z, Umetani M, Shaul PW, Morrison SJ. 27-Hydroxycholesterol induces hematopoietic stem cell mobilization and extramedullary hematopoiesis during pregnancy. J Clin Invest 2017; 127:3392-3401. [PMID: 28783041 DOI: 10.1172/jci94027] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 06/15/2017] [Indexed: 12/13/2022] Open
Abstract
Extramedullary hematopoiesis (EMH) is induced during pregnancy to support rapid expansion of maternal blood volume. EMH activation requires hematopoietic stem cell (HSC) proliferation and mobilization, processes that depend upon estrogen receptor α (ERα) in HSCs. Here we show that treating mice with estradiol to model estradiol increases during pregnancy induced HSC proliferation in the bone marrow but not HSC mobilization. Treatment with the alternative ERα ligand 27-hydroxycholesterol (27HC) induced ERα-dependent HSC mobilization and EMH but not HSC division in the bone marrow. During pregnancy, 27HC levels increased in hematopoietic stem/progenitor cells as a result of CYP27A1, a cholesterol hydroxylase. Cyp27a1-deficient mice had significantly reduced 27HC levels, HSC mobilization, and EMH during pregnancy but normal bone marrow hematopoiesis and EMH in response to bleeding or G-CSF treatment. Distinct hematopoietic stresses thus induce EMH through different mechanisms. Two different ERα ligands, estradiol and 27HC, work together to promote EMH during pregnancy, revealing a collaboration of hormonal and metabolic mechanisms as well as a physiological function for 27HC in normal mice.
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Affiliation(s)
- Hideyuki Oguro
- Children's Research Institute and.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Cellular Engineering, The Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA
| | - Jeffrey G McDonald
- Department of Molecular Genetics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Zhiyu Zhao
- Children's Research Institute and.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Michihisa Umetani
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, Texas, USA
| | - Philip W Shaul
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Center for Pulmonary and Vascular Biology and
| | - Sean J Morrison
- Children's Research Institute and.,Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.,Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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46
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Asare BK, Yawson E, Rajnarayanan RV. Flexible small molecular anti-estrogens with N,N-dialkylated-2,5-diethoxy-4-morpholinoaniline scaffold targets multiple estrogen receptor conformations. Cell Cycle 2017; 16:1465-1477. [PMID: 28723234 DOI: 10.1080/15384101.2017.1339848] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Estrogen mediates various cellular processes including cell proliferation, differentiation, growth and mammary gland function. Estrogen Receptors (ERs) are expressed in 70% of breast cancers. Consequently, estrogen mediated ER signaling plays a critical role in breast cancer diagnosis, prognosis, and treatment. ERs are ligand-triggered transcription factors. However, in the absence of a cognate estrogenic ligand, ERs can be activated by a variety of other extracellular signals. Tamoxifen, an anti-estrogen that selectively targets ER, induces substantial regression of breast tumors and an increase in disease-free survival. Tamoxifen mimics estrogen effects in other tissues thereby providing some beneficial effects including reduced risk of osteoporosis. However, breast cancers that initially respond well to tamoxifen tend to develop resistance and resume growth despite the continued presence of the antagonist. Library of compounds with substituted morpholinoaniline scaffold, a set of structurally divergent potential ER antagonists that fit the tamoxifen pharmacophore, were designed to target ER Ligand Binding Domain (LBD) and to recruit co-regulator proteins including BRCA1 over a range of conformational changes. Two of the lead compounds in the library, BR46 and BR47, were found to inhibit estrogen induced cell proliferation and cell viability. Discovery of novel lead molecules targeting ligand binding pockets of hER has provided structural clues toward the development of new breed of small molecule therapeutics for tamoxifen-resistant breast cancers and would complement already existent anti-estrogen therapy.
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Affiliation(s)
- Bethany K Asare
- a Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo, SUNY , Buffalo , NY , USA
| | - Emmanuel Yawson
- a Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo, SUNY , Buffalo , NY , USA
| | - Rajendram V Rajnarayanan
- a Department of Pharmacology and Toxicology, Jacobs School of Medicine and Biomedical Sciences , University at Buffalo, SUNY , Buffalo , NY , USA
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47
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Experimental and computational insights on the recognition mechanism between the estrogen receptor α with bisphenol compounds. Arch Toxicol 2017; 91:3897-3912. [DOI: 10.1007/s00204-017-2011-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/08/2017] [Indexed: 01/31/2023]
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48
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Souza PCT, Textor LC, Melo DC, Nascimento AS, Skaf MS, Polikarpov I. An alternative conformation of ERβ bound to estradiol reveals H12 in a stable antagonist position. Sci Rep 2017; 7:3509. [PMID: 28615710 PMCID: PMC5471280 DOI: 10.1038/s41598-017-03774-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 04/12/2017] [Indexed: 02/04/2023] Open
Abstract
The natural ligand 17β-estradiol (E2) is so far believed to induce a unique agonist-bound active conformation in the ligand binding domain (LBD) of the estrogen receptors (ERs). Both subtypes, ERα and ERβ, are transcriptionally activated in the presence of E2 with ERβ being somewhat less active than ERα under similar conditions. The molecular bases for this intriguing behavior are mainly attributed to subtype differences in the amino-terminal domain of these receptors. However, structural details that confer differences in the molecular response of ER LBDs to E2 still remain elusive. In this study, we present a new crystallographic structure of the ERβ LBD bound to E2 in which H12 assumes an alternative conformation that resembles antagonist ERs structures. Structural observations and molecular dynamics simulations jointly provide evidence that alternative ERβ H12 position could correspond to a stable conformation of the receptor under physiological pH conditions. Our findings shed light on the unexpected role of LBD in the lower functional response of ERβ subtype.
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Affiliation(s)
- Paulo C T Souza
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil.,Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Larissa C Textor
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil
| | - Denise C Melo
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil
| | - Alessandro S Nascimento
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil
| | - Munir S Skaf
- Institute of Chemistry, University of Campinas - UNICAMP, P. O. Box, 6154, Campinas, SP, Brazil.
| | - Igor Polikarpov
- São Carlos Institute of Physics, University of São Paulo - USP, P.O. Box 396, São Carlos, SP, Brazil.
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49
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Stender JD, Nwachukwu JC, Kastrati I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Rangarajan ES, Carlson KE, Katzenellenbogen JA, Yao XQ, Grant BJ, Leong HS, Lin CY, Frasor J, Nettles KW, Glass CK. Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells. Mol Cell 2017; 65:1122-1135.e5. [PMID: 28306507 PMCID: PMC5546241 DOI: 10.1016/j.molcel.2017.02.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 02/02/2017] [Accepted: 02/09/2017] [Indexed: 02/07/2023]
Abstract
Human breast cancers that exhibit high proportions of immune cells and elevated levels of pro-inflammatory cytokines predict poor prognosis. Here, we demonstrate that treatment of human MCF-7 breast cancer cells with pro-inflammatory cytokines results in ERα-dependent activation of gene expression and proliferation, in the absence of ligand or presence of 4OH-tamoxifen (TOT). Cytokine activation of ERα and endocrine resistance is dependent on phosphorylation of ERα at S305 in the hinge domain. Phosphorylation of S305 by IKKβ establishes an ERα cistrome that substantially overlaps with the estradiol (E2)-dependent ERα cistrome. Structural analyses suggest that S305-P forms a charge-linked bridge with the C-terminal F domain of ERα that enables inter-domain communication and constitutive activity from the N-terminal coactivator-binding site, revealing the structural basis of endocrine resistance. ERα therefore functions as a transcriptional effector of cytokine-induced IKKβ signaling, suggesting a mechanism through which the tumor microenvironment controls tumor progression and endocrine resistance.
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Affiliation(s)
- Joshua D Stender
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jerome C Nwachukwu
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Irida Kastrati
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Yohan Kim
- Department of Pathology and Laboratory Medicine, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Tobias Strid
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Maayan Yakir
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Sathish Srinivasan
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jason Nowak
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Tina Izard
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Erumbi S Rangarajan
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kathryn E Carlson
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - John A Katzenellenbogen
- Department of Chemistry, University of Illinois at Urbana-Champaign, 600 South Mathews Avenue, Urbana, IL 61801, USA
| | - Xin-Qiu Yao
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Barry J Grant
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Hon S Leong
- Department of Surgery, Schulich School of Medicine and Dentistry, Western University, London, ON N6A 5C1, Canada
| | - Chin-Yo Lin
- Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX 77204, USA
| | - Jonna Frasor
- Department of Physiology and Biophysics, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Kendall W Nettles
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
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50
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Wittmann HJ, Strasser A. Competitive association binding kinetic assays: a new tool to detect two different binding orientations of a ligand to its target protein under distinct conditions? Naunyn Schmiedebergs Arch Pharmacol 2017; 390:595-612. [DOI: 10.1007/s00210-017-1362-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/10/2017] [Indexed: 01/24/2023]
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