Structure-Based Discovery and Optimization of Benzo[d]isoxazole Derivatives as Potent and Selective BET Inhibitors for Potential Treatment of Castration-Resistant Prostate Cancer (CRPC)

Abstract

The bromodomain and extra-terminal (BET) family proteins have gained increasing interest as drug targets for treatment of castration-resistant prostate cancer (CRPC). Here, we describe the design, optimization, and evaluation of benzo[ d]isoxazole-containing compounds as potent BET bromodomain inhibitors. Cocrystal structures of the representative inhibitors in complex with BRD4(1) provided solid structural basis for compound optimization. The two most potent compounds, 6i (Y06036) and 7m (Y06137), bound to the BRD4(1) bromodomain with K values of 82 and 81 nM, respectively. They also exhibited high selectivity over other non-BET subfamily members. The compounds potently inhibited cell growth, colony formation, and the expression of AR, AR regulated genes, and MYC in prostate cancer cell lines. Compounds 6i and 7m also demonstrated therapeutic effects in a C4-2B CRPC xenograft tumor model in mice. These potent and selective BET inhibitors represent a new class of compounds for the development of potential therapeutics against CRPC.

Developing a variation of 3D‐QSAR/MD method in drug design

“…Moreover, nonpolar interactions were found between BRD4 hydrophobic residues (Trp 81, Leu 92, Leu 94, Cys 136, and Ile 146) and the inhibitor's nonpolar groups (as shown in Figure 2). These interaction patterns have been confirmed by MD simulations analysis, as shown later in Tables 2 and 3, in addition to confirming with other experimental studies, 51–55 which indicated the accuracy and reliability of the docking results. For better understanding, the general scheme and 3D‐structure for the interaction between BRD4 and C1 inhibitor were depicted in Figure 3.…”

“…The structure of BRD4 protein was obtained from RCSB protein database (PDB ID: 5Y8W) with 1.76 Å resolution 51 . After the preparation of initial BRD4 structures, including removing heteroatoms and cryptographic water molecules, a staged minimization was performed on the protein structure using Tripos forcefield and Powell method, implemented in SYBYL‐X v2.1 software 56,57 .…”

“…After the preparation of initial BRD4 structures, including removing heteroatoms and cryptographic water molecules, a staged minimization was performed on the protein structure using Tripos forcefield and Powell method, implemented in SYBYL‐X v2.1 software 56,57 . Then, the most effective BRD4 inhibitors were identified by exploring the recent literature 44,51–55 and their atomic coordinates were obtained from X‐ray crystallographic structures, available in PDB databases. The structures of the selected inhibitors were shown in Figure 1.…”

“…Therefore, inhibition of the acetyl‐lysine recognition site of BRD4 can be considered as a potential solution for the suppression of human cancer development 50 . Currently, numerous investigations have been performed related to the design of potential BRD4 inhibitors 51–55 . However, an effective inhibitor with a higher binding affinity toward BRD4 is still on demand and should be worked out.…”

Targeting Brd4 for cancer therapy: inhibitors and degraders

“…More recently, Xu's group described a series of benzo[d] isoxazole-containing compounds as potent Brd4 inhibitors. 58 Among them, compounds 41 and 42 showed the highest binding affinities to Brd4 1 , TGI values of 70% and 51% were achieved, respectively.…”