scholarly journals Flavonoids as Putative Epi-Modulators: Insight into Their Binding Mode with BRD4 Bromodomains Using Molecular Docking and Dynamics

Biomolecules ◽  
2018 ◽  
Vol 8 (3) ◽  
pp. 61 ◽  
Author(s):  
Fernando Prieto-Martínez ◽  
José Medina-Franco
Keyword(s):  
Kinase Inhibitors ◽  
Binding Mode ◽  
Binding Modes ◽  
Ligand Interaction ◽  
Bet Inhibitors ◽  
Protein Ligand Interaction ◽  
Brd4 Inhibition ◽  
Dynamics Simulations ◽  
Insight Into

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative, and antineoplastic activities. Recently, different studies showed that flavonoids have the potential to inhibit bromodomain and extraterminal (BET) bromodomains. Previous reports suggested that flavonoids bind between the Z and A loops of the bromodomain (ZA channel) due to their orientation and interactions with P86, V87, L92, L94, and N140. Herein, a comprehensive characterization of the binding modes of fisetin and the biflavonoid, amentoflavone, is discussed. To this end, both compounds were docked with BET bromodomain 4 (BRD4) using four docking programs. The results were post-processed with protein–ligand interaction fingerprints. To gain further insight into the binding mode of the two natural products, the docking results were further analyzed with molecular dynamics simulations. The results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was experimentally tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as the basis for scaffold optimization and the further characterization of flavonoids as BET inhibitors.

scholarly journals Flavonoids as Putative epi-modulators: Insights into their Binding Mode with BRD4 Bromodomain using Molecular Docking and Dynamics.

2018 ◽  
Author(s):  
Fernando Daniel Prieto-Martínez ◽  
José Luis Medina-Franco
Keyword(s):  
Kinase Inhibitors ◽  
Binding Mode ◽  
Ligand Interaction ◽  
Bet Inhibitors ◽  
Protein Ligand Interaction ◽  
Brd4 Inhibition ◽  
Molecular Dynamics Results ◽  
Molecular Docking And Dynamics ◽  
Micromolar Range

Flavonoids are widely recognized as natural polydrugs, given their anti-inflammatory, antioxidant, sedative and antineoplastic activities. Recently, different studies have shown that flavonoid have the potential to inhibit BET bromodomains. Previous reports suggest that flavonoids are putative inhibitors of the ZA channel due to their orientation and interactions with P86, V87, L92, L94 and N140. Herein, a comprehensive characterization of the binding mode of the biflavonoid amentoflavone and fisetin is discussed. To this end, both compounds were docked with BRD4 using four docking programs. Results were post-processed with protein-ligand interaction fingerprints. To gain further insights into the binding mode of the two natural products, docking results were further analyzed with molecular dynamics. Results showed that amentoflavone makes numerous contacts in the ZA channel, as previously described for flavonoids and kinase inhibitors. It was also found that amentoflavone can potentially make contacts with non-canonical residues for BET inhibition. Most of these contacts were not observed with fisetin. Based on these results, amentoflavone was tested for BRD4 inhibition, showing activity in the micromolar range. This work may serve as basis for scaffold optimization and further characterization of flavonoids as BET inhibitors.

scholarly journals SuCOS is Better than RMSD for Evaluating Fragment Elaboration and Docking Poses

2019 ◽  
Author(s):  
Susan Leung ◽  
Michael Bodkin ◽  
Frank von Delft ◽  
Paul Brennan ◽  
Garrett Morris
Keyword(s):  
Binding Mode ◽  
Docking Studies ◽  
Binding Modes ◽  
False Negatives ◽  
Ligand Interaction ◽  
Cross Docking ◽  
Protein Ligand Interaction ◽  
Feature Overlap ◽  
Better Than ◽  
Fragment Based Drug Discovery

One of the fundamental assumptions of fragment-based drug discovery is that the fragment’s binding mode will be conserved upon elaboration into larger compounds. The most common way of quantifying binding mode similarity is Root Mean Square Deviation (RMSD), but Protein Ligand Interaction Fingerprint (PLIF) similarity and shape-based metrics are sometimes used. We introduce SuCOS, an open-source shape and chemical feature overlap metric. We explore the strengths and weaknesses of RMSD, PLIF similarity, and SuCOS on a dataset of X-ray crystal structures of paired elaborated larger and smaller molecules bound to the same protein. Our redocking and cross-docking studies show that SuCOS is superior to RMSD and PLIF similarity. When redocking, SuCOS produces fewer false positives and false negatives than RMSD and PLIF similarity; and in cross-docking, SuCOS is better at differentiating experimentally-observed binding modes of an elaborated molecule given the pose of its non-elaborated counterpart. Finally we show that SuCOS performs better than AutoDock Vina at differentiating actives from decoy ligands using the DUD-E dataset. SuCOS is available at https://github.com/susanhleung/SuCOS . <br>

scholarly journals SuCOS is Better than RMSD for Evaluating Fragment Elaboration and Docking Poses

2019 ◽  
Author(s):  
Susan Leung ◽  
Michael Bodkin ◽  
Frank von Delft ◽  
Paul Brennan ◽  
Garrett Morris
Keyword(s):  
Binding Mode ◽  
Docking Studies ◽  
Binding Modes ◽  
False Negatives ◽  
Ligand Interaction ◽  
Cross Docking ◽  
Protein Ligand Interaction ◽  
Feature Overlap ◽  
Better Than ◽  
Fragment Based Drug Discovery

One of the fundamental assumptions of fragment-based drug discovery is that the fragment’s binding mode will be conserved upon elaboration into larger compounds. The most common way of quantifying binding mode similarity is Root Mean Square Deviation (RMSD), but Protein Ligand Interaction Fingerprint (PLIF) similarity and shape-based metrics are sometimes used. We introduce SuCOS, an open-source shape and chemical feature overlap metric. We explore the strengths and weaknesses of RMSD, PLIF similarity, and SuCOS on a dataset of X-ray crystal structures of paired elaborated larger and smaller molecules bound to the same protein. Our redocking and cross-docking studies show that SuCOS is superior to RMSD and PLIF similarity. When redocking, SuCOS produces fewer false positives and false negatives than RMSD and PLIF similarity; and in cross-docking, SuCOS is better at differentiating experimentally-observed binding modes of an elaborated molecule given the pose of its non-elaborated counterpart. Finally we show that SuCOS performs better than AutoDock Vina at differentiating actives from decoy ligands using the DUD-E dataset. SuCOS is available at https://github.com/susanhleung/SuCOS . <br>

scholarly journals Fragment-centric topographic mapping method guides the understanding of ABCG2-inhibitor interactions

RSC Advances ◽  
2019 ◽  
Vol 9 (14) ◽  
pp. 7757-7766 ◽  
Author(s):  
Yao Wu ◽  
Xin-Ying Gao ◽  
Xin-Hui Chen ◽  
Shao-Long Zhang ◽  
Wen-Juan Wang ◽  
...  
Keyword(s):  
Mapping Method ◽  
Topographic Mapping ◽  
Ligand Interaction ◽  
Mapping Tool ◽  
Protein Ligand Interaction ◽  
Insight Into ◽  
Computational Strategy

Our study gains insight into the development of novel specific ABCG2 inhibitors, and develops a comprehensive computational strategy to understand protein ligand interaction with the help of AlphaSpace, a fragment-centric topographic mapping tool.

Predicting Ligand Binding Modes from Neural Networks Trained on Protein–Ligand Interaction Fingerprints

2013 ◽  
Vol 53 (4) ◽  
pp. 763-772 ◽  
Author(s):  
Vladimir Chupakhin ◽  
Gilles Marcou ◽  
Igor Baskin ◽  
Alexandre Varnek ◽  
Didier Rognan
Keyword(s):  
Neural Networks ◽  
Ligand Binding ◽  
Binding Modes ◽  
Ligand Interaction ◽  
Protein Ligand Interaction ◽  
Interaction Fingerprints

scholarly journals Characterization of two distinct binding modes between syntaxin 4 and Munc18c

2009 ◽  
Vol 419 (3) ◽  
pp. 655-660 ◽  
Author(s):  
Veronica Aran ◽  
Fiona M. Brandie ◽  
Alasdair R. Boyd ◽  
Theodoros Kantidakis ◽  
Elizabeth J. Rideout ◽  
...  
Keyword(s):  
Protein Function ◽  
Binding Mode ◽  
Binding Modes ◽  
Sm Proteins ◽  
Apparent Lack ◽  
Protein Receptor ◽  
Syntaxin 4 ◽  
Vacuolar Protein ◽  
Sm Protein

Interaction of SM (Sec1/Munc18) proteins with their cognate syntaxins represents an important regulatory mechanism of SNARE (soluble N-ethylmaleimide-sensitive fusion protein-attachment protein receptor)-mediated membrane fusion. Understanding the conserved mechanisms by which SM proteins function in this process has proved challenging, largely due to an apparent lack of conservation of binding mechanisms between different SM–syntaxin pairs. In the present study, we have identified a hitherto uncharacterized mode of binding between syntaxin 4 and Munc18c that is independent of the binding mode shown previously to utilize the N-terminal peptide of syntaxin 4. Our data demonstrate that syntaxin 4 and Munc18c interact via two distinct modes of binding, analogous to those employed by syntaxin 1a–Munc18a and syntaxin 16–Vps45p (vacuolar protein sorting 45). These data support the notion that all syntaxin/SM proteins bind using conserved mechanisms, and pave the way for the formulation of unifying hypotheses of SM protein function.

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