Precision Targeting of pten-Null Triple-Negative Breast Tumors Guided by Electrophilic Metabolite Sensing

Abstract

Off-target effects continue to impede disease interventions, particularly when targeting a specific protein within a family of similar proteins, such as kinase isoforms that play tumor-subtype-specific roles in cancers. Exploiting the specific electrophilic-metabolite-sensing capability of Akt3, versus moderate or no sensing, respectively, by Akt2 and Akt1, we describe a first-in-class functionally Akt3-selective covalent inhibitor [MK-H­(F)­NE], wherein the electrophilic core is derived from the native reactive lipid metabolite HNE. Mechanistic profiling and pathway interrogations point to retention of the metabolite’s structureas opposed to implicit electrophilicityas being essential for biasing isoform preference, which we found translates to tumor-subtype specificity against pten-null triple-negative breast cancers (TNBCs). MK-H­(F)­NE further enables novel downstream target identification specific to Akt3-function in disease. In TNBC xenografts, MK-H­(F)­NE fares better than reversible pan-Akt-inhibitors and does not show commonly observed side-effects associated with Akt1-inhibition. Inhibitors derived from native-metabolite sensing are thus an enabling plan-of-action for unmasking kinase-isoform-biased molecular targets and tumor-subtype-specific interventions.

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities

“… 74,76,77 We recently made the first step to realizing this translational promise by using data from T-REX to design a first in class Akt3-selective covalent inhibitor. 78 …”

Time to Get Turned on by Chemical Biology

“…For instance, creating a chimera of a reactive pharmacophore mimicking a specific natural electrophile that dominantly inhibits the target protein, and a reversible binder to the target protein, allows meaningful irreversible inhibition of the target protein to be achieved at low inhibitor occupancy, through feedforward inhibition. Inhibition can manifest, even when a 1 : 1 mixture of an inhibitor‐resistant allele and the wild type sensitive allele are present in cells [14] . E) However, gain‐of‐function can generally intersect a disease‐causing process at any point on the pathway through any protein (pair); these traits make disease‐suppressing neofunctionalizations intriguing for drug discovery, but hard to identify.…”

“…Cartographing protein targets of specific electrophiles and ramifications of precision electrophile modifications of protein targets have illuminated signaling codes modulating disease‐relevant pathways at low ligand occupancy [40] . Honing protein targets of these polypharmacological species through chimeric drug design [41] has yielded new covalent Akt‐isoform‐specific inhibitors possessing dominant inhibition properties and improved efficacy in mice over traditional Akt inhibitors [14,42] . Such preliminary data could indicate that natural electrophiles are passkeys to unlock drugs whose effects are manifest even at low target occupancy.…”

“…Inhibition can manifest, even when a 1 : 1 mixture of an inhibitor-resistant allele and the wild type sensitive allele are present in cells. [14] E) However, gain-of-function can generally intersect a disease-causing process at any point on the pathway through any protein (pair); these traits make disease-suppressing neofunctionalizations intriguing for drug discovery, but hard to identify. F) CAR-T cells harness artificial protein expression to trigger gain of function causing intercellular signaling.…”

“…[40] Honing protein targets of these polypharmacological species through chimeric drug design [41] has yielded new covalent Akt-isoform-specific inhibitors possessing dominant inhibition properties and improved efficacy in mice over traditional Akt inhibitors. [14,42] Such preliminary data could indicate that natural electrophiles are passkeys to unlock drugs whose effects are manifest even at low target occupancy. Unnatural electrophiles have also started to show the ability to modulate protein activity in unexpected ways, such as stimulating their target's activity.…”