Selectively Targeting the Kinome-Conserved Lysine of PI3Kδ as a General Approach to Covalent Kinase Inhibition

Abstract

Selective covalent inhibition of kinases by targeting poorly conserved cysteines has proven highly fruitful to date in the development of chemical probes and approved drugs. However, this approach is limited to ∼200 kinases possessing such a cysteine near the ATP-binding pocket. Herein, we report a novel approach to achieve selective, irreversible kinase inhibition, by targeting the conserved catalytic lysine residue. We have illustrated our approach by developing selective, covalent PI3Kδ inhibitors that exhibit nanomolar potency in cellular assays, and a duration of action >48 h in CD4+ T cells. Despite conservation of the lysine residue throughout the kinome, the lead compound shows high levels of selectivity over a selection of lipid and protein kinases in biochemical assays, as well as covalent binding to very few off-target proteins in live-cell proteomic studies. We anticipate this approach could offer a general strategy, as an alternative to targeting non-conserved cysteines, for the development of selective covalent kinase inhibitors.

Covalent Small Molecules as Enabling Platforms for Drug Discovery

“…This general approach has also been used to profile the cysteine‐targeted covalent drugs afatinib (EGFR inhibitor) and ibrutinib (BTK inhibitor), as well as the newly developed third generation EGFR inhibitors osimertinib, PF‐06747775 and rociletinib . Additionally, a dichlorotriazine‐based probe has been utilised recently to label bromodomains on lysine and tyrosine residues, and the high selectivity profile of a lysine‐targeted covalent inhibitor of the lipid kinase PI3Kδ was also determined using similar strategies …”

“…Outside of the cysteine‐targeted realm, novel nucleophile‐electrophile pairs are rapidly emerging within the scientific literature, with the aim of expanding the toolkit of reactive modalities that are amenable to chemical biology and drug discovery (Figure ) . Notably, lysine has been pursued intensively with multiple publications detailing lysine‐reactive warheads such as activated esters, sulfur(VI)‐based reactive centres (sulfonyl fluorides and fluorosulfates) and α,β‐unsaturated systems . Some of these warheads can exhibit surprising aqueous stability, supporting their use in biological systems .…”

“…Notably, lysine has been pursued intensively with multiple publications detailing lysine‐reactive warheads such as activated esters, sulfur(VI)‐based reactive centres (sulfonyl fluorides and fluorosulfates) and α,β‐unsaturated systems . Some of these warheads can exhibit surprising aqueous stability, supporting their use in biological systems . Additionally, these warheads can result in improved selectivity relative to structurally related reversible inhibitors .…”

Reaktive chemische Sonden: Jenseits des Kinase‐Cysteinoms

“…Eine Analyse des Kinase‐Tyrosinoms zeigte das Vorliegen eines konservierten Tyrosinrests an der H5‐Position von 184 Kinasen, was den Schluss nahelegte, dass eine zu XO44 orthogonale halbwahllose Sonde entworfen werden könnte. Als Alternative könnten auch selektive chemische Sonden möglich sein, die den konservierten Lysinrest ansprechen, vorausgesetzt, die Bindung im Gleichgewicht ist optimiert …”

Cancer-targeted design of bioresponsive prodrug with enhanced cellular uptake to achieve precise cancer therapy

“…The DDS has attracted growing research interest over previous decades. It overcomes some of the limitations and barriers of traditional therapy (Mehmood et al., 2016 ; Dalton et al., 2018 ; Lin et al., 2018 ) and symbolizes that the pharmacologically active regimens were preferably selective and effective located at a pre-identified biological target in the vicinity of therapeutic window concentration but its access to non-target normal organs or tissues were limited; thus, toxic effects were minimized while the therapeutic index was maximized (Staben et al., 2016 ; Zhang et al., 2018 ). Our previous work has shown the great advantages of cancer-targeted inorganic carrier and nanocarrier platforms, such as excellent bioavailability, large surface area, and controlled release (Liu et al., 2015 ; Xie et al., 2017 ; Song et al., 2018 ; Zhao et al., 2018 ).…”