Exploiting Protein Conformational Change to Optimize Adenosine-Derived Inhibitors of HSP70

Abstract

HSP70 is a molecular chaperone and a key component of the heat-shock response. Because of its proposed importance in oncology, this protein has become a popular target for drug discovery, efforts which have as yet brought little success. This study demonstrates that adenosine-derived HSP70 inhibitors potentially bind to the protein with a novel mechanism of action, the stabilization by desolvation of an intramolecular salt-bridge which induces a conformational change in the protein, leading to high affinity ligands. We also demonstrate that through the application of this mechanism, adenosine-derived HSP70 inhibitors can be optimized in a rational manner.

Lysine‐Targeting Covalent Inhibitors

“…Further development of the electrophile led to sulfonyl fluoride 32, which was proposed to show greater reactivity through transition-state stabilization by Glu54 ( Figure 7D). [75] These proteins have become popular targets in oncology but have proven particularly difficult to inhibit owing to the high affinity of their endogenous substrates.I na na ttempt to develop cell-active chemical probes to study HSP70, we used rational design to modify the validated 8-N-benzyl adenosine reversible inhibitor 33 [76] with an electrophilic aliphatic acrylate,i nitially targeting ap roximal active site cysteine(Cys17;F igure 7E). [75] These proteins have become popular targets in oncology but have proven particularly difficult to inhibit owing to the high affinity of their endogenous substrates.I na na ttempt to develop cell-active chemical probes to study HSP70, we used rational design to modify the validated 8-N-benzyl adenosine reversible inhibitor 33 [76] with an electrophilic aliphatic acrylate,i nitially targeting ap roximal active site cysteine(Cys17;F igure 7E).…”

Pyrrolo[2,3‐d]pyrimidine (7‐deazapurine) as a privileged scaffold in design of antitumor and antiviral nucleosides

“…Recently, the mechanism of action of sangivamycin ( 5 ) in primary effusion lymphoma cells was studied showing that sangivamycin ( 5 ) acts through inhibition of Erk and Akt signaling in these cells . Sangivamycin ( 5 ) is also able to bind heat‐shock protein 70 (HSP70) (K D = 3.3 μM) which is a molecular chaperone with a proposed importance in oncology . Despite the attention paid to the naturally occurring 7‐deazapurine nucleosides, none of the compounds proceeded to clinical use.…”

An Irreversible Inhibitor of HSP72 that Unexpectedly Targets Lysine‐56

“…This process means the reactivity of the electrophilic warhead can be reduced, so the reaction is only fast once the complex has formed 8. We hypothesized that the validated nucleotide‐competitive 8‐ N ‐benzyladenosine 1 (Scheme 1),9 which is a potent targeted reversible inhibitor [Equation (2)], fulfills these criteria and could be modified for targeted covalent inhibitor design.$true\mathrm{normalE}+\mathrm{normalI}\underset{}{\overset{K{}_{\mathrm{l}}}{\leftrightarrow }}\mathrm{EI}\underset{}{\overset{k{}_{\mathrm{inact}}}{\to }}\mathrm{normalE}-\mathrm{normalI}$ $true\mathrm{normalE}+\mathrm{normalI}\underset{}{\overset{K{}_{\mathrm{i}}}{\leftrightarrow }}\mathrm{EI}$ $true\mathrm{normalE}+\mathrm{normalI}\underset{}{\overset{k{}_{\mathrm{inact}}}{\to }}\mathrm{normalE}-\mathrm{normalI}$ …”

“…HSP72 is a highly flexible protein, which complicates inhibitor design 9. The distance between Cys17 and the 5′‐position of the nucleoside analogues depends on the protein conformation, ranging from 9.2–10.7 Å (see Supporting Information).…”

“…However, two co‐crystal structures were solved, which represent two different reversible binding modes of the ligand in the open conformation of HSP72‐NBD 9. In both modes, 8 demonstrated the expected hydrogen‐bonding array of the adenine and ribose moieties, with the lipophilic para ‐chlorobenzylamine moiety parallel with the two α‐helices of the binding cleft 4.…”