Thermodynamic Dissection of Potency and Selectivity of Cytosolic Hsp90 Inhibitors

Abstract

The cytosolic Hsp90-selective inhibitor TAS-116 has an acceptable safety profile and promising antitumor activity in clinical trials. We examined the binding characteristics of TAS-116 and its analogs to determine the impact of the ligand binding mode on selectivity for cytosolic Hsp90. Analyses of the co-crystal structure of Hsp90 and inhibitor TAS-116 suggest that TAS-116 interacts with the ATP-binding pocket, the ATP lid region, and the hydrophobic pocket. A competitive isothermal titration calorimetry analysis confirmed that a small fragment of TAS-116 (THS-510) docks into the lid region and hydrophobic pockets without binding to the ATP-binding pocket. THS-510 exhibited enthalpy-driven binding to Hsp90α and selectively inhibited cytosolic Hsp90 activity. The heat capacity change of THS-510 binding was positive, likely due to the induced conformational rearrangement of Hsp90. Thus, we concluded that interactions with the hydrophobic pocket of Hsp90 determine potency and selectivity of TAS-116 and derivatives for the cytosolic Hsp90 isoform.

Pimitespib in patients with advanced gastrointestinal stromal tumor (CHAPTER-GIST-301): a randomized, double-blind, placebo-controlled phase III trial

“…8,9 Pimitespib (TAS-116) is an oral HSP90 inhibitor that selectively binds to cytoplasmic HSP90a and HSP90b. 10,11 Pimitespib inhibits growth and induces apoptosis in both imatinib-sensitive and -resistant GIST cell lines and reduces autophosphorylated mutated KIT in the Golgi apparatus. 12 A first-in-human phase I study determined the recommended dose of pimitespib and demonstrated its acceptable toxicity profile and promising clinical activity in patients with advanced solid tumors, including GIST.…”

Large-Scale Ligand Perturbations of the Protein Conformational Landscape Reveal State-Specific Interaction Hotspots

“…The position of the lid controls the accessibility of ligands to certain regions of the binding site . To extract general, state-specific binding hotspots, we probed whether the three major lid conformations form distinct binding-site surfaces.…”

“…The position of the lid controls the accessibility of ligands to certain regions of the binding site. 58 To extract general, state-specific binding hotspots, we probed whether the three major lid conformations form distinct binding-site surfaces. To find such hotspots, we calculated how often residues occurred within 5 Å of ligands bound to each lid conformation ( Figure 2 ).…”

“…Over the past 25 years, medicinal chemistry has tried to exploit this and produced 300 structures of Hsp90α-NTD bound to drug candidates or fragments in the Protein Data Bank (PDB) . Despite this rich structural dataset, comparative studies tend to consider too few conformational states or ligands − and may miss the bigger picture. No Hsp90α inhibitor has received FDA approval thus far.…”

Binding Mechanism of Inhibitors to Heat Shock Protein 90 Investigated by Multiple Independent Molecular Dynamics Simulations and Prediction of Binding Free Energy

“…In fact, both inhibitor binding and HSP90 chaperone cycles lead to large conformational changes in the flexible structure of HSP90 [ 26 , 27 , 28 ], which makes the design of a drug that can relieve side effects challenging. Moreover, multiple reports have indicated that the conformational changes in the N-terminal ATP site of HSP90 play a key role in the inhibition of ATP hydrolysis and client processing [ 29 , 30 , 31 , 32 ]. It is well known that the thermodynamics and kinetics of conformational changes are essential for gaining insights into the molecular mechanism of inhibitor–HSP90 binding and for the development of clinically available drugs against cancers [ 33 ].…”