Structural ensemble-based docking simulation and biophysical studies discovered new inhibitors of Hsp90 N-terminal domain

Hyun-Hwi Kim,Ja-Shil Hyun,Jun-Goo Jee,Joonhyeok Choi,Kwang-Eun Choi,Sung Jean Park

doi:10.1038/s41598-017-18332-8

Hyun-Hwi Kim, Ja-Shil Hyun + Show 4 more

Open Access

https://doi.org/10.1038/s41598-017-18332-8

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Abstract

Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and plays a substantial role in the folding of client proteins. The inhibition of Hsp90 has been regarded as an attractive therapeutic strategy for treating cancer because many oncogenic kinases are Hsp90 client proteins. In this study, we report new inhibitors that directly bind to N-terminal ATP-binding pocket of Hsp90. Optimized structure-based virtual screening predicted candidate molecules, which was followed by confirmation using biophysical and cell-based assays. Among the reported crystal structures, we chose the two structures that show the most favourable early enrichments of true-positives in the receiver operating characteristic curve. Four molecules showed significant changes in the signals of 2D [1H, 15N] correlation NMR spectroscopy. Differential scanning calorimetry analysis supported the results indicating direct binding. Quantified dissociation constant values of the molecules, determined by a series of 2D NMR experiments, lie in the range of 0.1–33 μM. Growth inhibition assay with breast and lung cancer cells confirmed the cellular activities of the molecules. Cheminformatics revealed that the molecules share limited chemical similarities with known inhibitors. Molecular dynamics simulations detailed the putative binding modes of the inhibitors.

Highlights

Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and accounts for 1–2% of the total amount of cytosolic protein
Inhibitors with crystal structures available in complex states were docked into the Hsp90N structures using six algorithms from five software programs [AutoDock[21], AutoDock Vina[22], DOCK 3.623, DOCK 6.724, and Glide-SP25,26]
The predicted poses that could be overlapped with the experimental ones within 2 Å of the root mean square deviation (RMSD) were judged as successful

Summary

Introduction

Heat shock protein 90 (Hsp90) is one of the most abundant cellular proteins and accounts for 1–2% of the total amount of cytosolic protein. The main role of Hsp[90] is to help the folding of client proteins as a chaperone. Through dynamic interactions with the client proteins, Hsp[90] participates in a wide range of cellular processes including protein assembly, trafficking, folding, and degradation. Hsp[90] exists as a dimer via intermolecular contacts between the Hsp90Cs. Hsp90M is thought to provide the main binding sites for client proteins. Most of the potential chemical inhibitors have focused on the ATP-binding site of Hsp90N. The structure of the complex with geldanamycin shows how the inhibitors causes the dissociation of the client kinase[12]. Structure-based virtual screening (SBVS) has played a complementary role in combination with high-throughput screening for discovering hit compounds in the early stages of the drug discovery process[18,19]. Computational studies, including cheminformatics and molecular dynamics (MD) simulation, were used to help elucidate the detailed features and roles of the identified moieties

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