A road map for prioritizing warheads for cysteine targeting covalent inhibitors

• Published in: European journal of medicinal chemistry Vol. 160; pp. 94 - 107
• Main Authors: Ábrányi-Balogh, Péter, Petri, László, Imre, Tímea, Szijj, Péter, Scarpino, Andrea, Hrast, Martina, Mitrović, Ana, Fonovič, Urša Pečar, Németh, Krisztina, Barreteau, Hélène, Roper, David I., Horváti, Kata, Ferenczy, György G., Kos, Janko, Ilaš, Janez, Gobec, Stanislav, Keserű, György M.
• Format: Journal Article
• Language: English
• Published: France Elsevier Masson SAS 05.12.2018; Elsevier
• Subjects: Alkyl and Aryl Transferases - antagonists & inhibitors; Alkyl and Aryl Transferases - metabolism; Cathepsin B; Cathepsin X; Covalent inhibitors; Cysteine - antagonists & inhibitors; Cysteine - chemistry; Dose-Response Relationship, Drug; Drug Design; Electrophilic warheads; Enzyme Inhibitors - chemical synthesis; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; GSH reactivity assay; Humans; Life Sciences; Ligands; Molecular Structure; MurA; Oligopeptide specificity assay; Structure-Activity Relationship; MurA; Covalent inhibitors; Cathepsin X; GSH reactivity assay; Electrophilic warheads; Cathepsin B; Oligopeptide specificity assay; selectivity; reactivity; proteases; cathepsin-b; kinase inhibitors; drug discovery; design; fragments; electrophiles
• ISSN: 0223-5234; 1768-3254; 1768-3254
• DOI: 10.1016/j.ejmech.2018.10.010

Targeted covalent inhibitors have become an integral part of a number of therapeutic protocols and are the subject of intense research. The mechanism of action of these compounds involves the formation of a covalent bond with protein nucleophiles, mostly cysteines. Given the abundance of cysteines in the proteome, the specificity of the covalent inhibitors is of utmost importance and requires careful optimization of the applied warheads. In most of the cysteine targeting covalent inhibitor programs the design strategy involves incorporating Michael acceptors into a ligand that is already known to bind non-covalently. In contrast, we suggest that the reactive warhead itself should be tailored to the reactivity of the specific cysteine being targeted, and we describe a strategy to achieve this goal. Here, we have extended and systematically explored the available organic chemistry toolbox and characterized a large number of warheads representing different chemistries. We demonstrate that in addition to the common Michael addition, there are other nucleophilic addition, addition-elimination, nucleophilic substitution and oxidation reactions suitable for specific covalent protein modification. Importantly, we reveal that warheads for these chemistries impact the reactivity and specificity of covalent fragments at both protein and proteome levels. By integrating surrogate reactivity and selectivity models and subsequent protein assays, we define a road map to help enable new or largely unexplored covalent chemistries for the optimization of cysteine targeting inhibitors. [Display omitted] •A broad library of cysteine targeting warheads was explored and characterized.•Diverse chemical reactions are suitable for specific covalent protein modification.•Warheads impact the reactivity and specificity of covalent fragments.•A road map for the optimization of cysteine targeting inhibitors is proposed.