Lysine‐Targeting Covalent Inhibitors

Abstract

Targeted covalent inhibitors have gained widespread attention in drug discovery as a validated method to circumvent acquired resistance in oncology. This strategy exploits small-molecule/protein crystal structures to design tightly binding ligands with appropriately positioned electrophilic warheads. Whilst most focus has been on targeting binding-site cysteine residues, targeting nucleophilic lysine residues can also represent a viable approach to irreversible inhibition. However, owing to the basicity of the ϵ-amino group in lysine, this strategy generates a number of specific challenges. Herein, we review the key principles for inhibitor design, give historical examples, and present recent developments that demonstrate the potential of lysine targeting for future drug discovery.

The Symbiotic Relationship Between Drug Discovery and Organic Chemistry

“…[264] Therefore, the design of targeted covalent modifiers relies on the use of "warheads" with well-balanced reactivity,w hich is revealed only in close proximity to the targetb inding center after appropriate positioning of the ligand provided by noncovalent interactions. [253,264,265] Because typical covalenti nhibitors address nucleophilic side chains of cysteineo rserine/threonine (less common cases include reactions with lysine, [266] histidine, methionine, or tyrosine residues [253] ), the list of most populari rreversible covalent warheadsi ncludes electrophilicm oieties, [253,261] such as Michael acceptors (a,b-unsaturated carbonyl compounds, acrylamides, vinyl sulfones, vinyl sulfonamides,e tc. ), compounds capable of formingS ÀSbonds (e.g.,thiols), sulfonyl fluorides, [267] epoxides, b-lactones and b-lactams, and alkylating agents.…”

Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues

“…[1,2] Aspirin, penicillin, omeprazole, and clopidogrel are examples of successful covalent drugs. [4,5] Imine formation is awell-known reaction of amines and several enzymes take advantage of Schiff base formation with ap yridoxal phosphate (PLP) cofactor. Recently,researchers at AstraZeneca have reported the generation of highly potent inhibitors of induced myeloid leukemia cell differentiation protein (Mcl-1), featuring af ormyl-or an acetyl-phenylboronic acid moiety in the ortho position.…”

Reactive Chemical Probes: Beyond the Kinase Cysteinome

“…Lysine labeling has been used extensively for bioconjugation and increasingly in the design of covalent inhibitors . Chemoproteomic applications of lysine targeting include the use of sulfo‐N‐hydroxy succinimide (NHS) biotin reagents, which contain the highly reactive NHS ester, to label cell‐surface proteins (cell permeation is deliberately impaired due to the presence of the charged sulfate group; Figure ).…”