Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo

Abstract

Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands, and in some cases, contribute towards selectivity. Bromodomains, small protein domains involved in the epigenetic regulation of gene transcription, display a network of four conserved water molecules in their binding pockets and have recently been the focus of intense medicinal chemistry efforts. Understanding why certain bromodomains have displaceable water molecules and others do not is extremely challenging, and it remains unclear which water molecules in a given bromodomain can be targeted for displacement. Here we estimate the stability of the conserved water molecules in 35 bromodomains via binding free energy calculations using all-atom grand canonical Monte Carlo simulations. Encouraging quantitative agreement to the available experimental evidence is found. We thus discuss the expected ease of water displacement in different bromodomains and the implications for ligand selectivity.

Molecular Basis for the N-Terminal Bromodomain-and-Extra-Terminal-Family Selectivity of a Dual Kinase–Bromodomain Inhibitor

“…Additionally, the fluorophenyl group sits much deeper in the binding pocket than those of previously reported BET inhibitors and is able to displace three water molecules present in the cocrystal structure of BRD4(1) with DMSO, in which one of these is a structurally conserved water. Our data and previous computational studies on the stability of bromodomain water networks 33,34 lead us to believe our observed selectivity profile also arises in part from the displacement of a conserved water from BRD4(1) and BRDT(1) but not from other BET bromodomains.…”

“…In these reports, the stabilities of bromodomain water networks have identified the water molecules most likely to be displaced in BRD4(1) and BRDT(1) among the other BET bromodomains, 33,34 whose water molecules are more tightly bound to the protein. Such an effect would also explain the observed selectivity of compound V for BRD4(1) and BRDT(1) over the other BETs measured in the ALPHAScreen assay.…”

A Chemical Toolbox for the Study of Bromodomains and Epigenetic Signaling

“…Interestingly, the Kac mimetic salicylic acid head group of PFI-3 and its derivatives showed selectivity for this bromodomain subfamily. This striking observation has been rationalized by the unique binding mode of family VIII inhibitors that penetrated deeper into the Kac binding site leading to displacement of water molecules that are maintained in other BRD-inhibitor complexes 58, 59 . In summary, BROMOscan ® offers a robust platform for accurate K D determination of BRD inhibitors, and chemical probes screened here maintained at least a 30-fold selectivity window against BRD in other families.…”

Discovery of a hidden transient state in all bromodomain families

“…Finally, we have superposed the closed state of our models with crystal structures that have drugs bound in the acetyl-lysine pocket, finding an excellent agreement between the pose of all drugs and the computed isosurfaces (see Supplementary Figures 2-6 and 9), including a deeply buried drug in SMARCA2, for which a set of conserved water molecules of the pocket are known to be displaceable. 43,47 Crystallographic evidence confirms the existence of the open state. To validate our results, we analyzed all the structures that are present in the bromodomain entry (PF00439) of the Pfam database, 48 accounting a total of 1.903 structures (see online materials for the complete list of PDBs).…”