Design of Reversible, Cysteine-Targeted Michael Acceptors Guided by Kinetic and Computational Analysis

• Published in: Journal of the American Chemical Society Vol. 136; no. 36; pp. 12624 - 12630
• Main Authors: Krishnan, Shyam, Miller, Rand M, Tian, Boxue, Mullins, R. Dyche, Jacobson, Matthew P, Taunton, Jack
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 10.09.2014; Amer Chemical Soc
• Subjects: Acrylonitrile - chemical synthesis; Acrylonitrile - chemistry; Acrylonitrile - pharmacology; Acrylonitriles; Affinity; Cell Line, Tumor; Chemistry; Chemistry, Multidisciplinary; Computation; Covalence; Cysteine - chemistry; Design engineering; Dose-Response Relationship, Drug; Humans; Inhibitors; Kinases; Models, Molecular; Molecular Structure; Physical Sciences; Protein Kinase Inhibitors - chemical synthesis; Protein Kinase Inhibitors - chemistry; Protein Kinase Inhibitors - pharmacology; Protein Kinases - metabolism; Protons; Science & Technology; Structure-Activity Relationship; Thiols; DRUG; COVALENT INHIBITORS; BETA-CYANO THIOETHERS; MECHANISMS; ELIMINATION-REACTIONS; ADDITIONS; RESIDUES; DISCOVERY; PROTEIN ADDUCTS
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/ja505194w

Electrophilic probes that covalently modify a cysteine thiol often show enhanced pharmacological potency and selectivity. Although reversible Michael acceptors have been reported, the structural requirements for reversibility are poorly understood. Here, we report a novel class of acrylonitrile-based Michael acceptors, activated by aryl or heteroaryl electron-withdrawing groups. We demonstrate that thiol adducts of these acrylonitriles undergo β-elimination at rates that span more than 3 orders of magnitude. These rates correlate inversely with the computed proton affinity of the corresponding carbanions, enabling the intrinsic reversibility of the thiol-Michael reaction to be tuned in a predictable manner. We apply these principles to the design of new reversible covalent kinase inhibitors with improved properties. A cocrystal structure of one such inhibitor reveals specific noncovalent interactions between the 1,2,4-triazole activating group and the kinase. Our experimental and computational study enables the design of new Michael acceptors, expanding the palette of reversible, cysteine-targeted electrophiles.