Discovery of potent heat shock protein 90 (Hsp90) inhibitors: structure-based virtual screening, molecular dynamics simulation, and biological evaluation

Figures & data

Figure 1. The chemical structures of known inhibitors of Hsp90.

Figure 2. The pharmacophore model of Hsp90. The hydrogen-bond donor (F1) and aromatic centre (F2) were indicated by green and orange spheres, respectively. The two hydrophobic centroid features F3 and F4 were indicated by yellow spheres. The dashed black line represented hydrogen-bond interaction. Each key residue was annotated with a three-letter amino acid code.

Figure 3. ROC curve of the generated Hsp90 pharmacophore model.

Figure 4. The protocol for virtual screening and biological evaluation of Hsp90 inhibitors.

Figure 5. The chemical structures of HPs 1–4.

Table 1. The drug-like properties, docking sores and biological data of HPs 1–4 and MPC-3100.

Name	MW	nHD	nHA	Log P(o/w)	Docking Score [kcal/mol]	IC50 (nM)^a
HP-1	405.83	4	7	2.41	–13.57	23.32 ± 1.77
HP-2	361.78	4	6	2.56	–13.45	44.91 ± 2.58
HP-3	436.30	4	6	3.05	–13.39	61.69 ± 3.06
HP-4	585.01	8	9	1.41	–13.71	17.64 ± 1.45
MPC-3100	549.44	2	7	2.89	–13.31	136.16 ± 4.27

^a The inhibitory effects of HPs 1–4 and positive control MPC-3100 on Hsp90 protein.

Figure 6. The docking modes of HPs 1–4 with key residues of Hsp90. (A) HP-1; (B) HP-2; (C) HP-3; (D) HP-4. The dashed black line represents hydrogen-bond interaction.

Figure 7. RMSD of atoms during MD simulations. (A, B) RMSDs of HP-1-Hps90 complexes and HP-1, respectively; (C, D) RMSDs of HP-2-Hps90 complexes and HP-2, respectively; (E, F) RMSDs of HP-3-Hps90 complexes and HP-3, respectively; (G, H) RMSDs of HP-4-Hps90 complexes and HP-4, respectively;.

Figure 8. (A–D) RMSF of Cα atoms of Hsp90 residues in HPs 1–4-Hsp90 complexes, respectively. The colour code is HP-1-Hsp90 (yellow), HP-2-Hsp90 (red), HP-3-Hsp90 (green), and HP-4-Hsp90 (bule). (E–H) Secondary structure of Hsp90 in HPs 1–4-Hsp90 complexes, respectively.

Figure 9. The docking modes of HPs 1–4 and the original ligand bind to the ATP-binding pocket of NTD of Hsp90.

Figure 10. The cytotoxicity of MPC-3100 and HPs 1–4 against human colon cancer HCT-116 cells.

Table 2. Biochemical profile of HP-4.

Assay	IC50 (nM)^a
HCT-116 cell proliferation	148.52
HeLa cell proliferation	206.39
A549 cell proliferation	210.81
A2780 cell proliferation	372.06
DU145 cell proliferation	289.14
HepG2 cell proliferation	337.92
A498 cell proliferation	254.17

^a IC₅₀ (nM) is the concentration of compound needed to reduce cell growth by 50% following 72 h cell treatment with HP-4.

Figure 11. In vivo anti-tumour effects of HP-4. Data are represented as mean ± SD, n = 5. ***p < 0.001.

Data availability statement

The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author/s.