Discovery of a hidden transient state in all bromodomain families

Abstract

Bromodomains (BDs) are small protein modules that interact with acetylated marks in histones.These post-translational modifications are pivotal to regulate gene expression, making BDs promising targets to treat several diseases. While the general structure of BDs is well known, their dynamical features and their interplay with other macromolecules are poorly understood, hampering the rational design of potent and selective inhibitors. Here we combine extensive molecular dynamics simulations, Markov state modeling and structural data to reveal a novel and transiently formed state that is conserved across all BD families. It involves the breaking of two backbone hydrogen bonds that anchor the ZA-loop with the α A helix, opening a cryptic pocket that partially occludes the one associated with histone binding. Our results suggest that this novel state is an allosteric regulatory switch for BDs, potentially related to a recently unveiled BD-DNA binding mode.

Differential BET Bromodomain Inhibition by Dihydropteridinone and Pyrimidodiazepinone Kinase Inhibitors

“…Sandwiched between the WPF shelf and a conserved leucine residue, optimal positioning of the inhibitor is likely influenced by the dynamics and flexibility of bromodomains. 23 It appears that the conglomerate of small changes in vdW distances between hydrophobic residues and inhibitor atoms beyond the warhead determines the overall shape that each inhibitor preferably adopts upon KAc site occupation (Figure 6). Depending on the length and number of rotatable bonds of the solubilizing moiety, the resulting conformational state of each inhibitor likely differs in energy and entropy contributions toward complex formation, consequently impacting binding affinity.…”

Macromolecular room temperature crystallography

“…To address this shortcoming, qFit-ligand was developed to find often isoenergetic, unmodeled conformations of drug-like molecules within crystal structures (van Zundert et al, 2018). For PDB structures of cancer target BRD4, the method revealed that as much as 29% of the protein crystal structures showed evidence of unmodeled protein-ligand interactions that would have been informative to guide compound design (Raich et al, 2020). Generally, one rarely finds ligand sites 100% occupied, as they are typically modeled.…”

Along the allostery stream: Recent advances in computational methods for allosteric drug discovery

“…[156][157][158][159][160] Identifying "hidden" allosteric sites using computational methods, such as MD simulations and Markov state model (MSM) analysis, has recently obtained considerable progresses. 66,[161][162][163][164][165] In the following section, we review computational advances with respect to revealing these two categories of allosteric sites (Table 2), with the aim of providing guidance for future related allosteric structural studies.…”

“…The former is readily observed within protein crystal structures and is therefore easy to detect, while the latter only transiently emerges throughout protein conformational dynamics and has thus been historically intractable by most experimental techniques 156–160 . Identifying “hidden” allosteric sites using computational methods, such as MD simulations and Markov state model (MSM) analysis, has recently obtained considerable progresses 66,161–165 . In the following section, we review computational advances with respect to revealing these two categories of allosteric sites (Table 2), with the aim of providing guidance for future related allosteric structural studies.…”