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Zare F, Solhjoo A, Sadeghpour H, Sakhteman A, Dehshahri A. Structure-based virtual screening, molecular docking, molecular dynamics simulation and MM/PBSA calculations towards identification of steroidal and non-steroidal selective glucocorticoid receptor modulators. J Biomol Struct Dyn 2023; 41:7640-7650. [PMID: 36134594 DOI: 10.1080/07391102.2022.2123392] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 10/14/2022]
Abstract
Glucocorticoids have been used in the treatment of many diseases including inflammatory and autoimmune diseases. Despite the wide therapeutic effects of synthetic glucocorticoids, the use of these compounds has been limited due to side effects such as osteoporosis, immunodeficiency, and hyperglycaemia. To this end, extensive studies have been performed to discover new glucocorticoid modulators with the aim of increasing affinity for the receptor and thus less side effects. In the present work, structure-based virtual screening was used for the identification of novel potent compounds with glucocorticoid effects. The molecules derived from ZINC database were screened on account of structural similarity with some glucocorticoid agonists as the template. Subsequently, molecular docking was performed on 200 selected compounds to obtain the best steroidal and non-steroidal conformations. Three compounds, namely ZINC_000002083318, ZINC_000253697499 and ZINC_000003845653, were selected with the binding energies of -11.5, -10.5, and -9.5 kcal/mol, respectively. Molecular dynamic simulations on superior structures were accomplished with the glucocorticoid receptor. Additionally, root mean square deviations, root mean square fluctuation, radius of gyration, hydrogen bonds, and binding-free energy analysis showed the binding stability of the proposed compounds compared to budesonide as an approved drug. The results demonstrated that all the compounds had suitable binding stability compared to budesonide, while ZINC_000002083318 showed a tighter binding energy compared to the other compounds.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fateme Zare
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Aida Solhjoo
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hossein Sadeghpour
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Sakhteman
- Department of Medicinal Chemistry, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali Dehshahri
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
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Hu X, Pang J, Chen C, Jiang D, Shen C, Chai X, Yang L, Zhang X, Xu L, Cui S, Hou T, Li D. Discovery of novel non-steroidal selective glucocorticoid receptor modulators by structure- and IGN-based virtual screening, structural optimization, and biological evaluation. Eur J Med Chem 2022; 237:114382. [PMID: 35483323 DOI: 10.1016/j.ejmech.2022.114382] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/09/2022] [Accepted: 04/09/2022] [Indexed: 11/04/2022]
Abstract
Glucocorticoids (GCs) are the most commonly used anti-inflammatory drugs. However, their excellent therapeutic effects are often accompanied by undesirable side effects. To discover selective glucocorticoid receptor modulators (SGRMs) that preferentially induce transrepression with little or no transactivation activity, a structure-based virtual screening by combining molecular docking and InteractionGraphNet (IGN) rescoring was performed, and compound HP210 was identified. HP210 did not induce the transactivation functions of GR while still acted on the NF-κB mediated tethered transrepression function (IC50 = 2.32 μM), and suppressed the secretion of pro-inflammation cytokines IL-1β and IL-6. Compared with dexamethasone, HP210 showed no cross activities with phylogenetically related mineralcorticoid receptor and progesterone receptor and no significant effect on osteoprotegerin, exhibiting a reduced side-effect profile. Then, guided by the molecular dynamics simulations and binding free energy calculations, compound HP210_b4 with over two-fold higher transrepression activity (IC50 = 0.99 μM) was discovered. This study reported a group of non-steroidal new-scaffold SGRMs, providing valuable clues for the development of novel anti-inflammatory drugs.
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Affiliation(s)
- Xueping Hu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Jinping Pang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Changwei Chen
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Dejun Jiang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Chao Shen
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xin Chai
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Liu Yang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Xujun Zhang
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Lei Xu
- Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou, 213001, China
| | - Sunliang Cui
- Institute of Drug Discovery and Design, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, Zhejiang, China
| | - Tingjun Hou
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China; State Key Lab of CAD&CG, Zhejiang University, Hangzhou, Zhejiang, 310058, China
| | - Dan Li
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang, 310058, China.
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Predicting Potential Endocrine Disrupting Chemicals Binding to Estrogen Receptor α (ERα) Using a Pipeline Combining Structure-Based and Ligand-Based in Silico Methods. Int J Mol Sci 2021; 22:ijms22062846. [PMID: 33799614 PMCID: PMC7999354 DOI: 10.3390/ijms22062846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/08/2021] [Accepted: 03/08/2021] [Indexed: 02/07/2023] Open
Abstract
The estrogen receptors α (ERα) are transcription factors involved in several physiological processes belonging to the nuclear receptors (NRs) protein family. Besides the endogenous ligands, several other chemicals are able to bind to those receptors. Among them are endocrine disrupting chemicals (EDCs) that can trigger toxicological pathways. Many studies have focused on predicting EDCs based on their ability to bind NRs; mainly, estrogen receptors (ER), thyroid hormones receptors (TR), androgen receptors (AR), glucocorticoid receptors (GR), and peroxisome proliferator-activated receptors gamma (PPARγ). In this work, we suggest a pipeline designed for the prediction of ERα binding activity. The flagged compounds can be further explored using experimental techniques to assess their potential to be EDCs. The pipeline is a combination of structure based (docking and pharmacophore models) and ligand based (pharmacophore models) methods. The models have been constructed using the Environmental Protection Agency (EPA) data encompassing a large number of structurally diverse compounds. A validation step was then achieved using two external databases: the NR-DBIND (Nuclear Receptors DataBase Including Negative Data) and the EADB (Estrogenic Activity DataBase). Different combination protocols were explored. Results showed that the combination of models performed better than each model taken individually. The consensus protocol that reached values of 0.81 and 0.54 for sensitivity and specificity, respectively, was the best suited for our toxicological study. Insights and recommendations were drawn to alleviate the screening quality of other projects focusing on ERα binding predictions.
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Yung KC, Xu CW, Zhang ZW, Yu WJ, Li Q, Xu XR, Han YF, Wang XJ, Yin J. Investigation on glucocorticoid receptors within platelets from adult patients with immune thrombocytopenia. Hematology 2020; 25:37-42. [PMID: 31905108 DOI: 10.1080/16078454.2019.1710025] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Objective: The expression of glucocorticoid receptors within platelets from newly diagnosed Immune Thrombocytopenia (ITP) patients in the adult was investigated.Methods: GR expression in platelets from newly diagnosed ITP patients and healthy controls was measured using flow cytometry. Subsequently, platelets RNA and proteins were isolated and used for confirming the flow cytometry results by using RT-qPCR and ELISA.Results: Flow cytometry showed that the percentages of platelets expressing GRα and GRβ from ITP patients were significantly higher than those from healthy controls (P < 0.05). qPCR and ELISA confirmed that GRα and GRβ were increased at both RNA transcription and protein expression levels within platelets from ITP patients compared with healthy controls.Conclusion: We speculated that the up-regulation of glucocorticoid receptor within platelets may be an important biological feature of platelets in patients with ITP, and may also play an important role in the treatment of ITP, which is worthy of further study.
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Affiliation(s)
- Kam Chau Yung
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Cheng Wei Xu
- Hemodialysis Room, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Ze Wen Zhang
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Wen Jun Yu
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Qian Li
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Xian Ru Xu
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Ya Fei Han
- Department of Spine Surgery, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Xin Jia Wang
- Department of Spine Surgery, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
| | - Jun Yin
- Division of Hematology, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
- Department of Clinical Laboratory Medicine, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
- Translational Medicine Research Center, the Second Affiliated Hospital of Shantou University Medical College, Shantou, People's Republic of China
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Significance estimation for sequence-based chemical similarity searching (PhAST) and application to AuroraA kinase inhibitors. Future Med Chem 2013; 4:1897-906. [PMID: 23088272 DOI: 10.4155/fmc.12.148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Chemical similarity searching allows the retrieval of preferred screening molecules from a compound database. Candidates are ranked according to their similarity to a reference compound (query). Assessing the statistical significance of chemical similarity scores helps prioritizing significant hits, and identifying cases where the database does not contain any promising compounds. METHOD Our text-based similarity measure, Pharmacophore Alignment Search Tool (PhAST), employs pair-wise sequence alignment. We adapted the concept of E-values as significance estimates and employed a sampling technique that incorporates the principle of importance sampling in a Markov chain Monte Carlo simulation to generate distributions of random alignment scores. These distributions were used to compute significance estimates for similarity scores in a preliminary prospective virtual screen for inhibitors of Aurora A kinase. CONCLUSION Assessing the significance of compound similarity computed with PhAST allows for a statistically motivated identification of candidate screening compounds. Inhibitors of Aurora A kinase were retrieved from a large compound library.
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Onnis V, Kinsella GK, Carta G, Jagoe WN, Price T, Williams DC, Fayne D, Lloyd DG. Virtual screening for the identification of novel nonsteroidal glucocorticoid modulators. J Med Chem 2010; 53:3065-74. [PMID: 20334371 DOI: 10.1021/jm901452y] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we describe the first application of ligand-based drug design (LBDD) to the derivation of a predictive pharmacophore for the human glucocorticoid receptor (hGR). Creation of a four feature pharmacophore in Catalyst was subsequently validated through a virtual screen of 264000 commercially available compounds. From a selected hit list of 11 diverse compounds, two nonsteroidal molecules demonstrated low micromolar activity against hGR as validated through fluorescence polarization competitive assay. Additionally, these compounds were tested for their trans-repression potential by their ability to inhibit IL-1 induced, IL-6 expression in the human A549 lung epithelial cell line. Co-treatment of A549 with 21 (MDG169) (10 microM) in combination with dexamethasone showed an improved inhibitory effect when compared to dexamethasone alone with the cooperative effect being dependent on the dexamethasone dose. Putative binding orientations in the hGR ligand binding domain crystal structure are presented. These compounds represent novel nonsteroidal hGR modulating scaffolds, rationally identified through ligand-focused computational modeling.
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Affiliation(s)
- Valeria Onnis
- Molecular Design Group, School of Biochemistry and Immunology, Trinity College Dublin, Dublin 2, Ireland
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