ArticleFrontiers in pharmacology2018
Structural Changes Due to Antagonist Binding in Ligand Binding Pocket of Androgen Receptor Elucidated Through Molecular Dynamics Simulations.
Article in Frontiers in pharmacology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 39 citations in OpenAlex.
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- Molecular Targets of Minor Cannabinoids in Breast Cancer: In Silico and In Vitro Studies.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Systematic computational strategies for identifying protein targets and lead discovery.RSC medicinal chemistry · 2024Review
- Study of Glabranin as an Inhibitor Against Prostate Cancer: Molecular Docking, Molecular Dynamics Simulation, MM-PBSA Calculation and QSAR Prediction.Indian journal of clinical biochemistry : IJCB · 2024Article
- Decoding the κ Opioid Receptor (KOR): Advancements in Structural Understanding and Implications for Opioid Analgesic Development.Molecules (Basel, Switzerland) · 2024Review
- Luteolin inhibits A549 cells proliferation and migration by down-regulating androgen receptors.European journal of medical research · 2023Article
- Three-Dimensional Structural Insights Have Revealed the Distinct Binding Interactions of Agonists, Partial Agonists, and Antagonists with the µ Opioid Receptor.International journal of molecular sciences · 2023Review
- PARP7 mono-ADP-ribosylates the agonist conformation of the androgen receptor in the nucleus.The Biochemical journal · 2021Article
- Binding of Androgen- and Estrogen-Like Flavonoids to Their Cognate (Non)Nuclear Receptors: A Comparison by Computational Prediction.Molecules (Basel, Switzerland) · 2021Article
- New Insights into the Binding Mechanism of Co-regulator BUD31 to AR AF2 Site: Structural Determination and Analysis of the Mutation Effect.Current computer-aided drug design · 2020Article
- Discovery of a Novel Natural Allosteric Inhibitor That Targets NDM-1 AgainstFrontiers in pharmacology · 2020Article
- Structural Dynamics of Agonist and Antagonist Binding to the Androgen Receptor.The journal of physical chemistry. B · 2019Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
When a small molecule binds to the androgen receptor (AR), a conformational change can occur which impacts subsequent binding of co-regulator proteins and DNA. In order to accurately study this mechanism, the scientific community needs a crystal structure of the Wild type AR (WT-AR) ligand binding domain, bound with antagonist. To address this open need, we leveraged molecular docking and molecular dynamics (MD) simulations to construct a structure of the WT-AR ligand binding domain bound with antagonist bicalutamide. The structure of mutant AR (Mut-AR) bound with this same antagonist informed this study. After molecular docking analysis pinpointed the suitable binding orientation of a ligand in AR, the model was further optimized through 1 μs of MD simulations. Using this approach, three molecular systems were studied: (1) WT-AR bound with agonist R1881, (2) WT-AR bound with antagonist bicalutamide, and (3) Mut-AR bound with bicalutamide. Our structures were very similar to the experimentally determined structures of both WT-AR with R1881 and Mut-AR with bicalutamide, demonstrating the trustworthiness of this approach. In our model, when WT-AR is bound with bicalutamide, Val716/Lys720/Gln733, or Met734/Gln738/Glu897 move and thus disturb the positive and negative charge clumps of the AF2 site. This disruption of the AF2 site is key for understanding the impact of antagonist binding on subsequent co-regulator binding. In conclusion, the antagonist induced structural changes in WT-AR detailed in this study will enable further AR research and will facilitate AR targeting drug discovery.
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