Discovery of Potent Disheveled/Dvl Inhibitors Using Virtual Screening Optimized With NMR-Based Docking Performance Index

Abstract

Most solid tumors have their own cancer stem cells (CSCs), which are resistant to standard chemo-therapies. Recent reports have described that Wnt pathway plays a key role in self-renewal and tumorigenesis of CSCs. Regarding the Wnt/β-catenin pathway, Dvl (mammalian Disheveled) is an attractive target of drug discovery. After analyzing the PDZ domain of human Dvl1 (Dvl1-PDZ) using NMR, we subjected it to preliminary NMR titration studies with 17 potential PDZ-binding molecules including CalBioChem-322338, a commercially available Dvl PDZ domain inhibitor. Next, we performed virtual screening (VS) using the program GOLD with nine parameter sets. Results were evaluated using the NMR-derived docking performance index (NMR-DPI). One parameter set of GOLD docking showing the best NMR-DPI was selected and used for the second VS against 5,135 compounds. The second docking trial identified more than 1,700 compounds that exhibited higher scores than CalBioChem-322338. Subsequent NMR titration experiments with five new candidate molecules (NPL-4001, 4004, 4011, 4012, and 4013), Dvl1-PDZ revealed larger chemical shift changes than those of CalBioChem-322338. Finally, these compounds showed partial proliferation inhibition activity against BT-20, a triple negative breast cancer (TNBC) cell. These compounds are promising Wnt pathway inhibitors that are potentially useful for anti-TNBC therapy.

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling

“…For comparison, four compounds shown in Supporting Information Figure S6 were assayed by ITC (Supporting Information Figure S7) regarding their affinity to Dvl-3 PDZ. Ky-02327 was already determined to bind with a Kd of 8.3 ± 0.8 µM Surprisingly, CBC-322338/3289-8625 showed very low affinity, with a Kd above 400 µM (assumed to be the threshold for our ITC assay), which was larger than the originally reported value (10.6 +/-1.7) (Grandy 2009) and closer to the value found by Hori et al (Hori 2018…”

“…12.5 ± 0.5 -5.9 0.7 -6.8 4.7 ± 0.2 -8. and 21 respectively. Compounds NPL-1011 (Hori 2018), and Sulindac , CBC-322338/3289-8625 (Grandy 2009, Hori 2018, and NSC668036 (Shan 2005), for more thermodynamic parameters see Supporting Information Figure S7. For Ky-02327 the value from literature is included.…”

Bone marrow mesenchymal stem cells promote prostate cancer cell stemness via cell–cell contact to activate the Jagged1/Notch1 pathway

“…3 The Fifth Department of Chemotherapy, Guangxi Medical University Cancer Hospital, Hedi road 71, Nanning 530021, Guangxi Zhuang Autonomous Region, China. 4 Department of Urology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, China.…”

“…Most solid tumors, including PCa, contain a small subpopulation of pluripotent cancer stem cells (CSCs) that possess the characteristics of self-renewal, unlimited proliferation, and aggressive tumorigenicity [ 4 ]. Notably, the existence of CSCs may be associated with the initiation, progression, local recurrence, and distant metastasis of solid tumors [ 5 ], which are common causes of the high incidence and final death for most patients with advanced PCa.…”

Small-molecule inhibitors of the PDZ domain of Dishevelled proteins interrupt Wnt signalling

“…For further operations with descriptors, an Euclidian metric was introduced. Shape descriptors were distributed into 6 clusters using the k-means algorithm (Jain and Dubes, 1988). For each cluster, a centroid structure was defined as the one whose descrip- tor is the closest to mean descriptor for the cluster.…”