Binding Kinetics versus Affinities in BRD4 Inhibition

Zhou, Jingwei; Wang, Laiyou; Liu, Zhihong; Guo, Jiao; Wu, Ruibo

doi:10.1021/acs.jcim.5b00265

Cited by 26 publications

(23 citation statements)

References 52 publications

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“…Comparing RMSFs between apo and holo BDs in both systems, we found that BC loop almost kept unchangeable during the simulation, whereas the flexibility of ZA loop notably decreased upon binding to RVX-208. It is in accordance with the previously reported results of other inhibitor-BD systems 37 , 38 . The higher flexibility decreasing of ZA loop of BD2 relative to BD1 indicated that BD2 pocket might undergo conformational rearrangement due to the binding of RVX-208.…”

Section: Resultssupporting

confidence: 94%

Selective inhibition mechanism of RVX-208 to the second bromodomain of bromo and extraterminal proteins: insight from microsecond molecular dynamics simulations

Wang

Liu

et al. 2017

Sci Rep

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RVX-208 is a recently reported inhibitor of bromo and extraterminal (BET) family proteins (including BRD2-4 and BRDT) with selectivity for the second bromodomain (BD2), currently in phase III clinical trials. Despite of its promising antitumor activity, due to the conserved folds of the first and second bromodomains (BD1 and BD2), the detailed selectivity mechanism of RVX-208 towards BD2 over BD1 is still unknown. To elucidate selective inhibition mechanism of RVX-208 to BD2, microsecond molecular dynamics simulations were performed in this study for BRD2-BD1, BRD2-BD2 and BRD4-BD1 with and without RVX-208, respectively. Binding free energy calculations show that there exists strongest interaction between RVX-208 and BRD2-BD2. Leu383 and Asn429 are two most important residues of BRD2-BD2 for binding to RVX-208. Structural network analysis reveals that RVX-208 can shorten the communication path of ZA and BC loops in BRD2-BD2 pocket, making pocket more suitable to accommodate RVX-208. Additionally, different behaviors of His433 (Asp160 in BRD2-BD1) and Val435 (Ile162 in BRD2-BD1) in BRD2-BD2 are key factors responsible for selective binding of RVX-208 to BRD2-BD2. The proposed selective inhibition mechanism of RVX-208 to BRD2-BD2 can be helpful for rational design of novel selective inhibitors of the second bromodomain of BET family proteins.

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Section: Resultssupporting

confidence: 94%

Selective inhibition mechanism of RVX-208 to the second bromodomain of bromo and extraterminal proteins: insight from microsecond molecular dynamics simulations

Wang

Liu

et al. 2017

Sci Rep

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“…27 This protein is particularly suitable for this type of calculation, since the ligands bind near its surface and with clear access to the solvent, avoiding steric clashes during the pulling process. It is worth noting that the first BRD4 bromodomain has already been the target of numerous computational studies on ligand binding, using a range of methods such as fragment-based docking, 33 the MM-PBSA/GBSA method combined with steered molecular dynamics (SMD), 34 and free energy techniques, such as umbrella sampling, 35 ABF, 21 and alchemical methods. 11 In this last study, Aldeghi et al computed the binding free energies of several molecules to the BRD4 bromodomain, starting both from the crystal structure complexes and the binding poses obtained after performing protein–ligand rigid docking, and obtained encouraging agreement with experiment.…”

Section: Introductionmentioning

confidence: 99%

“…A similar procedure was also performed for a series of additional bromodomains. 18 In another computational study, Kuang et al 35 noted a conformational change in the protein’s ZA-loop, which occurs in the absence of bound ligands and produces an apo conformation slightly different from the crystal structure. In the present study, as part of the binding free energy calculations, we also investigate conformational changes in the apo protein, using the APR method to obtain the free energies associated with this process.…”

Section: Introductionmentioning

confidence: 99%

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

Heinzelmann

Henriksen

Gilson

2017

J. Chem. Theory Comput.

122

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Bromodomains, protein domains involved in epigenetic regulation, are able to bind small molecules with high affinity. In the present study, we report free energy calculations for the binding of seven ligands to the first BRD4 bromodomain, using the attach-pull-release (APR) method to compute the reversible work of removing the ligands from the binding site and then allowing the protein to relax conformationally. We test three different water models, TIP3P, TIP4PEw, and SPC/E, as well as the GAFF and GAFF2 parameter sets for the ligands. Our simulations show that the apo crystal structure of BRD4 is only metastable, with a structural transition happening in the absence of the ligand typically after 20 ns of simulation. We compute the free energy change for this transition with a separate APR calculation on the free protein and include its contribution to the ligand binding free energies, which generally causes an underestimation of the affinities. By testing different water models and ligand parameters, we are also able to assess their influence in our results and determine which one produces the best agreement with the experimental data. Both free energies associated with the conformational change and ligand binding are affected by the choice of water model, with the two sets of ligand parameters affecting their binding free energies to a lesser degree. Across all six combinations of water model and ligand potential function, the Pearson correlation coefficients between calculated and experimental binding free energies range from 0.55 to 0.83, and the root-mean-square errors range from 1.4–3.2 kcal/mol. The current protocol also yields encouraging preliminary results when used to assess the relative stability of ligand poses generated by docking or other methods, as illustrated for two different ligands. Our method takes advantage of the high performance provided by graphics processing units and can readily be applied to other ligands as well as other protein systems.

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“… 11 Functionally, it acts as a chromatin reader that specifically recognizes the acetylated lysine in histone tails and facilitates the localization of chromatin regulatory cofactors, thereby regulating transcription initiation and elongation. 12 , 13 BRD4 also serves as a mitotic bookmark and plays a key role in cell cycle progression. 14 Ectopic expression of BRD4 in cultured cells results in G1/S arrest, while inhibition of BRD4 function by injection of anti-BRD4 antibodies arrests cells in G2/M phase.…”

mentioning

confidence: 99%

BRD4 as a therapeutic target for nonfunctioning and growth hormone pituitary adenoma

et al. 2020

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Background Nonfunctioning pituitary adenoma (NFPA) and growth hormone pituitary adenoma (GHPA) are major subtypes of pituitary adenomas (PAs). The primary treatment is surgical resection. However, radical excision remains challenging, and few effective medical therapies are available. It is urgent to find novel targets for the treatment. Bromodomain-containing protein 4 (BRD4) is an epigenetic regulator that leads to aberrant transcriptional activation of oncogenes. Herein, we investigated the pathological role of BRD4 and evaluated the effectiveness of BRD4 inhibitors in the treatment of NFPA and GHPA. Methods The expression of BRD4 was detected in NFPA, GHPA, and normal pituitary tissues. The efficacies of BRD4 inhibitors were evaluated in GH3 and MMQ cell lines, patient-derived tumor cells, and in vivo mouse xenograft models of PA. Standard western blots, real-time PCR, and flow cytometry experiments were performed to investigate the effect of BRD4 inhibitors on cell cycle progression, apoptosis, and the expression patterns of downstream genes. Results Immunohistochemistry studies demonstrated the overexpression of BRD4 in NFPA and GHPA. In vitro and in vivo studies showed that treatment with the BRD4 inhibitor ZBC-260 significantly inhibited the proliferation of PA cells. Further mechanistic studies revealed that ZBC-260 could downregulate the expression of c-Myc, B-cell lymphoma 2 (Bcl2), and related genes, which are vital factors in pituitary tumorigenesis. Conclusion In this study, we determined the overexpression of BRD4 in NFPA and GHPA and assessed the effects of BRD4 inhibitors on PA cells in vitro and in vivo. Our findings suggest that BRD4 is a promising therapeutic target for NFPA and GHPA. Key Points 1. BRD4 is overexpressed in NFPA and GHPA. 2. BRD4 inhibitors reduced PA cell proliferation in vitro and in vivo.

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Binding Kinetics versus Affinities in BRD4 Inhibition

Cited by 26 publications

References 52 publications

Selective inhibition mechanism of RVX-208 to the second bromodomain of bromo and extraterminal proteins: insight from microsecond molecular dynamics simulations

Selective inhibition mechanism of RVX-208 to the second bromodomain of bromo and extraterminal proteins: insight from microsecond molecular dynamics simulations

Attach-Pull-Release Calculations of Ligand Binding and Conformational Changes on the First BRD4 Bromodomain

BRD4 as a therapeutic target for nonfunctioning and growth hormone pituitary adenoma

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