Molecular Dynamics Simulations Reveal the Mechanisms of Allosteric Activation of Hsp90 by Designed Ligands

Abstract

Controlling biochemical pathways through chemically designed modulators may provide novel opportunities to develop therapeutic drugs and chemical tools. The underlying challenge is to design new molecular entities able to act as allosteric chemical switches that selectively turn on/off functions by modulating the conformational dynamics of their target protein. We examine the origins of the stimulation of ATPase and closure kinetics in the molecular chaperone Hsp90 by allosteric modulators through atomistic molecular dynamics (MD) simulations and analysis of protein-ligand interactions. In particular, we focus on the cross-talk between allosteric ligands and protein conformations and its effect on the dynamic properties of the chaperone’s active state. We examine the impact of different allosteric modulators on the stability, structural and internal dynamics properties of Hsp90 closed state. A critical aspect of this study is the development of a quantitative model that correlates Hsp90 activation to the presence of a certain compound, making use of information on the dynamic adaptation of protein conformations to the presence of the ligand, which allows to capture conformational states relevant in the activation process. We discuss the implications of considering the conformational dialogue between allosteric ligands and protein conformations for the design of new functional modulators.

Design of Allosteric Stimulators of the Hsp90 ATPase as New Anticancer Leads

“…Compounds 20 – 23 , characterized by the presence of a bulky substituent on the amino group, display the lowest activity. The compounds 22 and 23 with an N ‐methylpiperazine group on the phenol side chain, stimulate ATPase to a degree comparable to that induced by the glycosidic derivatives previously tested, suggesting that the six‐membered ring actually mimics sugar substituents. Maximal stimulatory effects were observed for 24 , 25 , and 26 indicating that minimizing the steric hindrance on the amine‐pharmacophore, but maintaining its alkylation, is beneficial to adenosine triphosphatase (ATPase) stimulation, resulting in a 4–5 fold increase…”

“…This method facilitated the design of modulators showing promising anticancer activities and a novel molecular mechanism of perturbation of Hsp90 functions: the ligands, in fact, were synthesized and experimentally proved to be activators of closure kinetics and ATPase activity of the chaperone in vitro, to induce cancer cell death, and to interfere with client maturation . We developed a first quantitative structure–dynamics–activity–relationship (QSDAR) model correlating the structures of an initial set of modulators to observed activation effects …”

“…Such modification resulted in an improved anticancer cytotoxicity of the ligands. A new round of MD simulations and allosteric coordination analysis supported the importance of interactions with E477 and D503 . Here, to establish structure–dynamics–activity relationships, in the absence of crystal structures difficult to obtain due to the flexibility of the system, we directed design efforts towards obtaining different amine substitutions on the phenyl‐benzofuran scaffold.…”

Targeting the Hsp90 C-terminal domain to induce allosteric inhibition and selective client downregulation

“…Since in silico modeling cannot explain the oligomerization process, further investigation is required to probe the mechanistic details. Hsp90 appears to have multiple allosteric regulation points that are part of its conformational cycle; these may be modulated by interactions with co-chaperones [82,83] and mutations appear to affect oligomerization [83]. Although Hsp90 is a homodimer, it also exists in other oligomeric forms that are important for its biological activity including the ability to interact with clients and/or co-chaperones [66,84,85].…”

Designing Molecular Spanners to Throw in the Protein Networks

“…These concepts were successfully used to discover and optimize a set of allosteric activators of the important chaperone Hsp90 (Figure ) . Comparative analyses of allosteric activators (Figure , left) and inhibitors (Figure , right) showed that the ligands induced different dynamics states and conformational ensembles in the protein, responsible for different functional responses . One of the Hsp90 activators is illustrated in Scheme (compound 26 ) …”