Computational protocol: N,N Dimethylacetamide a drug excipient that acts as bromodomain ligand for osteoporosis treatment

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Protocol publication

[…] Apo crystals of the BRD4-BD1 bromodomain were grown at 4 °C using the hanging drop vapor diffusion method under the condition 0.2 M Sodium Nitrate, 20% PEG 3350, 10% ethylene glycol. The apo crystals were then soaked with 10% (V/V) DMA overnight and flash-frozen for measurements. Data sets were collected on a PILATUS 16 M detector at the Swiss Light Source beamline X06SA of the Paul Scherrer Institute (Villigen, Switzerland) and indexed, integrated and scaled with the XDS and CCP4 programs. The structures were solved by molecular replacement with PHASER using the BRD4 structure (PDB entry 4PCI) as a search model and refined with PHENIX. The atomic coordinates and structure factors of BRD4 in complex with DMA have been deposited into the Protein Data Bank as entry 5HCL.Data collection and refinement statistics are given (). [...] All statistical analysis were performed with IBM SPSS statistics 22. Results are expressed as the mean ± SD and were compared by the non-parametric Kruskal-Wallis-Test followed by the Mann-Whitney- U Test. Results were considered significantly different for P < 0.05. […]

Pipeline specifications

Software tools XDS, CCP4, PHENIX, SPSS
Applications Miscellaneous, Small-angle scattering, Protein structure analysis
Diseases Osteoporosis