The Alkyne Moiety as a Latent Electrophile in Irreversible Covalent Small Molecule Inhibitors of Cathepsin K

Abstract

Irreversible covalent inhibitors can have a beneficial pharmacokinetic/pharmacodynamics profile but are still often avoided due to the risk of indiscriminate covalent reactivity and the resulting adverse effects. To overcome this potential liability, we introduced an alkyne moiety as a latent electrophile into small molecule inhibitors of cathepsin K (CatK). Alkyne-based inhibitors do not show indiscriminate thiol reactivity but potently inhibit CatK protease activity by formation of an irreversible covalent bond with the catalytic cysteine residue, confirmed by crystal structure analysis. The rate of covalent bond formation ( k inact ) does not correlate with electrophilicity of the alkyne moiety, indicative of a proximity-driven reactivity. Inhibition of CatK-mediated bone resorption is validated in human osteoclasts. Together, this work illustrates the potential of alkynes as latent electrophiles in small molecule inhibitors, enabling the development of irreversible covalent inhibitors with an improved safety profile.

Ubiquitin C‐Terminal Hydrolase L1: Biochemical and Cellular Characterization of a Covalent Cyanopyrrolidine‐Based Inhibitor

“…The reactive free energies of various nitriles have been calculated computationally, and the reaction energy of a cyanamide such as in molecule 1 is higher than a typical nitrile, though such an electrophile is known to be reversible . To confirm that compound 1 is indeed a covalent modifier of UCHL1 and assess the rate of reversibility, we performed a jump‐dilution experiment in which UCHL1 was pre‐incubated with 1 at 7 μ m , approximately tenfold the IC 50 value, for 30 minutes. The enzyme‐inhibitor complex was then rapidly diluted 100‐fold into a solution containing Ub‐Rho.…”

The Ugi Three‐Component Reaction; a Valuable Tool in Modern Organic Synthesis

“…Enantiomeric pure α‐aminoamides, except from their well‐known utility with protein synthesis, [ 89 ] hold without any doubt significant roles as subunits in biological active molecules, [ 90,91 ] natural products [ 92 ] and drugs. [ 93 ] Other applications can also be found in their use as catalysts, [ 94 ] co‐catalysts [ 95 ] and ligands [ 96,97 ] in transition metal chemistry.…”

Covalent Small Molecules as Enabling Platforms for Drug Discovery

“…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 .…”