Molecular Dynamics Simulations of Bromodomains Reveal Binding‐Site Flexibility and Multiple Binding Modes of the Natural Ligand Acetyl‐Lysine

Abstract

Experimental protein structures provide spatial information at the atomic level. A further dimension, time, is supplemented by molecular dynamics. Since the pioneering work on the 58‐residue inhibitor of bovine pancreatic trypsin in the group of Martin Karplus in the seventies, molecular dynamics simulations have shown that the intrinsic flexibility of proteins is essential for their function. Here, we review simulation studies of bromodomains. These protein modules are involved in the recognition of acetylated lysine side chains, a post‐translational modification frequently observed in histone tails. The molecular dynamics simulations have unmasked: (i) the large plasticity of the loops lining the acetyl‐lysine binding site (coupled to its self‐occlusion), and (ii) multiple binding modes of acetyl‐lysine. These simulation results suggest that recognition of histone tails by bromodomains is modulated by their intrinsic flexibility, and further corroborate the utility of molecular dynamics in understanding (macro)molecular recognition.

Observed bromodomain flexibility reveals histone peptide- and small molecule ligand-compatible forms of ATAD2

“…We focused on co-crystallization rather than soaking technique, and extensive characterization of the H4K5ac complex revealed an unexpected conformational change accompanying the peptide recognition and provided an undescribed ATAD2A form in a closed state. Including structural data from a novel empty form of ATAD2A bromodomain we compared a total of 6 states, confirming experimentally the evidence of protein dynamics that has been described by molecular dynamics simulation [19], and providing a snapshot of the mechanism for peptide recognition and accompanying loop flexibility. With the recent identification of ATAD2A small-molecule binders by our lab and others [20, 21], our study highlights that conformational flexibility of the bromodomain of ATAD2A has implications for histone-peptide recognition towards the development of ATAD2A bromodomain inhibitors.…”

“…Despite packing constrains, an X-ray structure obtained by peptide soaking confirmed the interaction [20]. Because recent molecular dynamics studies suggested some flexibility of the ZA and BC loop on bromodomains [19], in the present study we prioritized a co-crystallization strategy. We identified alternative crystallogenesis conditions and obtained the complex by co-crystallization.…”

“…2a). Computational studies have suggested apparent bromodomain flexibility [19, 33, 34], however no loop rearrangements have been described experimentally in the bromodomain family upon histone binding, describing an additional mode of molecular recognition for bromodomains. Thus, we decided to compare the movement of each loop in detail.…”

Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain

“…More importantly, the replacement of the carboxylic acid by a tetrazole as isoster (15) 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 EP300 (Table 2), are consistent with the fact that identical residues are present in the acetyllysine binding site of both proteins. Compounds 23 and 24 were synthesized ( Figure 3) to explore the effect of the amide direction (23) and the presence of an N-methyl carboxamide as a surrogate of the acetyl moiety (24), 31 respectively. In both cases a decrease in affinity for CREBBP was observed, confirming the excellent shape complementarity between the acetyl benzene moiety and the acetyl-lysine binding site of the CREBBP bromodomain and its paralogue EP300.…”

“…20 Absolute stereocontrol was required to attain the desired potency and still only moderate selectivity against BRD4(1), the most promiscuous bromodomain, was found. Recently, Hay 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 3 We decided to take a different approach based on high-throughput docking on the target 22,23 and started our CREBBP ligand-identification campaign by fragment-based docking into the structure of the CREBBP bromodomain. Herein we present the result of a computer-aided, structure-based approach which has enabled the discovery of several nM ligands of the CREBBP bromodomain upon optimization of binding by modulation of the electrostatic interaction with Arg1173 (numbering from PDB structures 3SVH and 3P1C), a residue located at the entrance of the binding site that is considered to be key for attaining selectivity towards CREBBP.…”