New Cysteine Covalent Modification Strategies Enable Advancement of Proteome‐wide Selectivity of Kinase Modulators

Abstract

There has been tremendous progress in covalent inhibitors as evidenced by the ascent of innovative electrophilic warheads with suppressed non-specific reactivity but enhanced capacity for proximity-driven covalent reactions with nucleophilic residues in the targeted site. Kinases, a central player in cancers, autoimmune disorders and chronic diseases, represent a highly targeted class of enzymes by covalent inhibitors. However, innovative strategies to afford high selectivity in target recognition remain a pressing need. This minireview focuses on four promising strategies to achieve superior target selectivity through rational design of the covalent engagement. Special emphasis is placed on examples where the selectivity had arisen by complementing the reactivity of protein cysteines with electrophilic warheads specified for distinct covalent chemistry, or inspired from native electrophile signalling in cells.[a] I. Guan

A Comprehensive Guide for Assessing Covalent Inhibition in Enzymatic Assays Illustrated with Kinetic Simulations

“…Drug development of irreversible covalent inhibitors is typically geared towards simultaneous improvement of the binding affinity (reflected in a lower K I value) and faster covalent bond formation (reflected in a higher k inact value) to generate irreversible covalent inhibitors with a high k inact /K I value for the desired enzyme target (Mah, Thomas, & Shafer, 2014; Schwartz et al., 2014), while minimizing the intrinsic reactivity with undesired enzymes such as GSH (Guan, Williams, Pan, & Liu, 2021; Lonsdale et al., 2017; Martin, MacKenzie, Fletcher, & Gilbert, 2019). Typical reported k inact /K I values of irreversible inhibitors range from 10 5 ‐10 7 M −1 s −1 for kinase inhibitors (Schwartz et al., 2014; Telliez et al., 2016; Zhai, Ward, Doig, & Argyrou, 2020), 10 1 ‐10 5 M −1 s −1 for protease inhibitors (Meara & Rich, 1995; Mons et al., 2019; Rocha‐Pereira et al., 2014), 10 2 ‐10 4 M −1 s −1 for other target classes (Fell et al., 2020; Hansen et al., 2018; Lanman et al., 2020), to 10 −2 ‐10 2 M −1 s −1 for covalent fragments (Johansson et al., 2019; Kathman, Xu, & Statsyuk, 2014).…”

Synthesis and structure–activity relationship of berkeleylactone A-derived antibiotics

“…Since the nature of the reactive Michael acceptors is likely to translate into their problematic in vivo stability and toxicity, labile sulfa-adducts to Michael acceptors have recently attracted increasing attention as potential covalently modified (pro)drugs. 18 As confirmed, berkeleylactone A readily undergoes retro-sulfa-Michael addition, thus regenerating the 4-oxocrotonic motif. 12 However, berkeleylactone A exhibits more potent antimicrobial activity than the closely related A26771B, found in the same fungal coculture and explicitly featuring the oxocrotonyl system.…”

Isoform‐Selective Fluorescent Labeling of 14‐3‐3σ by Acrylamide‐Containing Fusicoccins

“…[10] We envisioned that FC derivatives bearing an electrophilic reactive group at the glucose moiety may irreversibly react with Cys38 in 14-3-3σ upon formation of the ternary complex with a mode-3 phospholigand. Although a number of cysteinedirected reactive groups have been developed, [15][16][17] the acrylamide group has been widely exploited in medicinal applications ranging from fragment-based drug discovery [18] to clinically used pharmaceuticals, including inhibitors for kinases [17] and K-Ras. [19] Thus, a series of FC derivatives, in which a fluorescent dye and an acrylamide group were introduced via a lysine spacer, was designed (1-3, Figure 2a).…”