In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4

Abstract

Bromodomains (BrDs), a conserved structural module in chromatin‐associated proteins, are well known for recognizing ε‐N‐acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD containing protein (BrD1 and BrD2) that plays a critical role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biological functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow‐up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole‐based compounds as BRD4 BrD1 inhibitors. Additionally, we investigated the molecular basis for Olinone's selective recognition by BrD1 over BrD2. Molecular dynamics simulations, free energy calculations, and conformational analyses of the apo‐BRD4‐BrD1|2 and BRD4‐BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds number and in mobility of the ZA and BC loops of the acetyl‐lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer‐aided molecular design techniques can effectively guide the development of small‐molecule BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivatives.

Targeting Bromodomain and Extraterminal Proteins for Drug Discovery: From Current Progress to Technological Development

“…Many BD1-selective inhibitors have been discovered, including Olinone ( 1 ) , and MS436 ( 2 ), with the 3D crystal structure of the latter with BRD4-BD1 also shown on the right (Figure A). ZL0580 ( 3 ) (IC 50 = 163 nM), a BRD4 BD1-selective inhibitor, was discovered by structure-guided drug design .…”

Inhibitors of bromodomain and extra‐terminal proteins for treating multiple human diseases

“…The configuration of Olinone within the BD1-binding pocket, its specific contact with five key residue replacements between BD1 and BD2, and the number and mobility of hydrogen bonds in the ZA and BC loops drive its BD1 selectivity. 37,202 Though Olinone is the most well-known BD1 selective BETi, other scaffolds, configurations, and binding to unique amino acid residues within a given BD pocket can also be selective F I G U R E 3 A, X-ray crystal structure of BRD4/BD1, outlined. B, X-ray crystal structure of BRD4/BD1 and BRD4/BD2 showing key residue replacements between bromodomains, with the example of apabetalone's (RVX-208) BD2-specific His433 binding (yellow arrows) for BD1 over BD2.…”

“…The most recognized example of a BD1 selective compound, Olinone, exhibits over 100‐fold higher binding affinity to BD1 than BD2 in all BET proteins. The configuration of Olinone within the BD1‐binding pocket, its specific contact with five key residue replacements between BD1 and BD2, and the number and mobility of hydrogen bonds in the ZA and BC loops drive its BD1 selectivity 37,202 . Though Olinone is the most well‐known BD1 selective BETi, other scaffolds, configurations, and binding to unique amino acid residues within a given BD pocket can also be selective for BD1 over BD2 156,203,204 …”

“…Bromodomain and extra‐terminal (BET) proteins are epigenetic “readers” that recognize and bind posttranslational modifications on histones and other transcriptional machinery to facilitate gene expression. BET proteins have received an increasing amount of attention in recent years, 1–49 and BET inhibitor(s) (BETi) that target the BET bromodomains (BD) are unique in drug development in that they are consecutively undergoing clinical investigation in vastly different disease areas. Evidence is mounting to support the use of BETi in treating cancer, metabolic, inflammatory, neurologic, cardiovascular, and musculoskeletal diseases 1–3,14,19,20,29,31,44,50–62 .…”

Binding selectivity of inhibitors toward the first over the second bromodomain of BRD4: theoretical insights from free energy calculations and multiple short molecular dynamics simulations

“…For instance, Zhou et al adopted MD simulations and binding free energy calculations to study binding selectivity of Olinone toward the first over the second bromodomain of BRD4. 45 Su et al applied MD simulations and molecular mechanics Poisson Boltzmann surface area (MM/PBSA) calculations to investigate binding selectivity of inhibitors toward two domains of BRD4. 46 However, the conformations sampled by cMD simulations possibly fall into a local minimum space, resulting in an insufficient sampling of protein conformations.…”