Dual-target inhibitors of bromodomain and extra-terminal proteins in cancer: A review from medicinal chemistry perspectives

Abstract

Bromodomain-containing protein 4 (BRD4), as the most studied member of the bromodomain and extra-terminal (BET) family, is a chromatin reader protein interpreting epigenetic codes through binding to acetylated histones and non-histone proteins, thereby regulating diverse cellular processes including cell cycle, cell differentiation, and cell proliferation. As a promising drug target, BRD4 function is closely related to cancer, inflammation, cardiovascular disease, and liver fibrosis. Currently, clinical resistance to BET inhibitors has limited their applications but synergistic antitumor effects have been observed when used in combination with other tumor inhibitors targeting additional cellular components such as PLK1, HDAC, CDK, and PARP1. Therefore, designing dual-target inhibitors of BET bromodomains is a rational strategy in cancer treatment to increase potency and reduce drug resistance. This review summarizes the protein structures and biological functions of BRD4 and discusses recent advances of dual BET inhibitors from a medicinal chemistry perspective. We also discuss the current design and discovery strategies for dual BET inhibitors, providing insight into potential discovery of additional dual-target BET inhibitors.

Keywords: bromodomain and extra-terminal (BET); bromodomain-containing protein 4; dual-target inhibitors; medicinal chemistry; structure-activity relationship.

FIGURE 1

Schematic diagram of BRD4 domain features and crystal structures. (A) Domain architecture of three BRD4 protein isoforms. (B) Crystal structure of BRD4(1) (PDB ID: 3MXF). (C) Crystal structure of BRD4(2) (PDB ID: 5U2C). (D) NMR structure of the BRD4 ET domain (PDB ID: 6BNH). Protein is represented by blue ribbons with WPF shelf residues indicated by yellow sticks

FIGURE 2

Schematic diagram of gene regulation and protein interactome networks of BRD4. (A) Schematic diagram of BRD4 gene-regulatory networks. (B) Schematic diagram of BRD4 interactome. BCL2, B-cell lymphoma 2; BD2, bromodomain 2; BID, basic residue-enriched interaction domain; BRD2, bromodomain-containing protein 2; BRD3, bromodomain-containing protein 3; BRD4, bromodomain-containing protein 4; BRD8, bromodomain-containing protein 8; BRDT, bromodomain testis-specific protein; BRPF3, bromodomain and PHD finger-containing protein 3; CAMKK2, calcium/calmodulin-dependent protein kinase kinase 2; CCL2, C-C motif chemokine ligand 2; CCNT1, cyclin T1; CDH15, cadherin 15; C-MYC, myelocytomatosis viral oncogene cellular homolog; CDK9, cyclin-dependent kinase 9; CK2, casein kinase II; DDX18, DEAD-box helicase 18; E2F, early 2 factor; FOSL1, fos like 1; GAS7, growth arrest specific 7; GREB1, growth regulating estrogen receptor binding 1; HMOX1, heme oxygenase 1; HTRA1, HtrA serine peptidase 1; IGFBP1, insulin-like growth factor-binding protein 1; IL-2, interleukin-2; IL-8, interleukin-8; INO80B, INO80 complex subunit B; KDM1B, lysine demethylase 1B; KEAP1, Kelch-like ECH-associated protein 1; KMT5B, lysine methyltransferase 5B; MYCN, myelocytomatosis viral oncogene neuroblastoma-derived homolog; NAA35, N-alpha-acetyltransferase 35; NPM1, nucleophosmin1; NPS, N-terminal cluster of CK2 phosphorylation sites; NRF2, nuclear factor erythroid 2-related factor 2; NSD2, nuclear receptor binding SET domain protein 2; NSD3, nuclear receptor binding SET domain protein 3; PSA, puromycin-sensitive aminopeptidase; P-TEFb, positive transcription elongation factor b; RFC3, replication factor C subunit 3; ROS, reactive oxygen species; SP110, SP110 nuclear body protein; TEX43, testis-expressed 43; TFF1, trefoil factor 1; ZNF740, zinc finger protein 740

FIGURE 3

Dual-target inhibitors of BET bromodomains and CDKs. (A) Chemical structures of dinaciclib, flavopiridol and compound 3. (B) X ray cocrystal structure of Dinaciclib bound to BRD4(1) (PDB ID: 4O70). (C) X ray cocrystal structure of dinaciclib bound to CDK2 (PDB ID: 4KD1). (D) X ray cocrystal structure of Flavopiridol bound to BRD4 (PDB ID: 4O71). (E) X ray cocrystal structure of flavopiridol bound to CDK9/cyclin T1 (PDB ID: 3BLR). Protein is represented by gray ribbons, with key compound-contacting residues indicated by yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red; Cl, green). Black dashed line = hydrogen bond; orange sphere = water molecule

FIGURE 4

Development of dual-target inhibitors of BET bromodomains and PLK1. (A) X ray cocrystal structure of BI-2536 bound to BRD4(1) (PDB ID: 4O74). (B) X ray cocrystal structure of BI-2536 bound to PLK1 (PDB ID: 2RKU). (C) SARs of BI-2536. Protein is represented by gray ribbons with key compound-contacting residues highlighted in yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red). Black dashed line = hydrogen bond; orange sphere = water molecule

FIGURE 5

Other dual-target inhibitors of BET bromodomains and PLK1

FIGURE 6

Design and SARs of dual-target inhibitors of BET bromodomains and ALK. (A) BI-2536 forms key interaction with BRD4 (blue) and PLK1 (green). (B) SARs of dual-target inhibitors of BET bromodomains and ALK. (C) X ray cocrystal structure of compound 9–6 bound to BRD4(1) (PDB ID: 6Q3Z). Protein is represented by gray ribbons with key compound-contacting residues highlighted in yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red; S, yellow). Black dashed line = hydrogen bond; orange sphere = water molecule

FIGURE 7

Development of dual inhibitors of BET bromodomains and JAK2. (A) Chemical structures of TG101348 and TG101209. (B) X ray cocrystal structure of TG101348 bound to BRD4(1) (PDB ID: 4OGJ). (C) SARs of dual inhibitors of BET bromodomains and JAK2. Protein is represented by gray ribbons, with key compound-contacting residues indicated by yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red; S, yellow). Black dashed line = hydrogen bond; orange sphere = water molecule

FIGURE 8

Dual-target inhibitors of BET bromodomains and PI3K. (A) Chemical structures of dual inhibitors of BET bromodomains and PI3K. (B) X ray cocrystal structure of SF2523 bound to BRD4(1) (PDB ID: 5U28). (C) X ray cocrystal structure of SF2558HA bound to BRD4(2) (PDB ID: 5U2C). Protein is represented by gray ribbons, with compound-contacting residues indicated by yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red; S, yellow). Black dashed line = hydrogen bond; orange sphere = water molecule

FIGURE 9

Dual-target inhibitors of BET bromodomains and p38 kinase

FIGURE 10

Dual-target inhibitors of BET bromodomains and other kinases

FIGURE 11

Design of dual-target inhibitors of BET and HDAC based on a pharmacophore fusion strategy. (A) The pharmacophore model of HDACi. (B) Design of compounds 41 and 42. X ray cocrystal structure of JQ1 bound to BRD4(1) (PDB ID: 3MXF). (C) Design of compounds 44, 45, and 46. X ray cocrystal structure of ABBV-744 bound to BRD2(2) (PDB ID: 6E6J). Protein is represented by light blue surface, with compound-contacting residues indicated by yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red; Cl, green; F, light cyan). Black dashed line = hydrogen bond

FIGURE 12

Design and SARs of dual-target inhibitors of BET and HDAC based on a pharmacophore fusion strategy (tetrahydroquinoline skeleton, quinolinone skeleton, and N6-benzoyladenine skeleton)

FIGURE 13

Design and SARs of dual-target inhibitors of BET and HDAC based on the pharmacophore fusion strategy (3,5-dimethylisoxazole skeleton and indole skeleton). Protein is represented by light blue surface, with compound-contacting residues indicated by yellow sticks. The compound is shown in sticks and colored according to the atom type (C, light blue; N, blue; O, red). Black dashed line = hydrogen bond

FIGURE 14

Design and SARs of dual-target inhibitors of BET/HDAC based on pharmacophore fusion of the thieno[2,3-d] pyrimidine skeleton

FIGURE 15

Dual-target inhibitors of BET bromodomains and other non-kinases and dual PROTAC of BET and PLK1