Combined Biophysical Chemistry Reveals a New Covalent Inhibitor with a Low-Reactivity Alkyl Halide

Abstract

17β-Hydroxysteroid dehydrogenase type 1 (17β-HSD1) plays a pivotal role in the progression of estrogen-related diseases because of its involvement in the biosynthesis of estradiol (E2), constituting a valuable therapeutic target for endocrine treatment. In the present study, we successfully cocrystallized the enzyme with the reversible inhibitor 2-methoxy-16β-( m-carbamoylbenzyl)-E2 (2-MeO-CC-156) as well as the enzyme with the irreversible inhibitor 3-(2-bromoethyl)-16β-( m-carbamoylbenzyl)-17β-hydroxy-1,3,5(10)-estratriene (PBRM). The structures of ternary complexes of 17β-HSD1-2-MeO-CC-156-NADP and 17β-HSD1-PBRM-NADP comparatively show the formation of a covalent bond between His and the bromoethyl side chain of the inhibitor in the PBRM structure. A dynamic process including beneficial molecular interactions that favor the specific binding of a low-reactivity inhibitor and subsequent N-alkylation event through the participation of His in the enzyme catalytic site clearly demonstrates the covalent bond formation. This finding opens the door to a new design of alkyl halide-based specific covalent inhibitors as potential therapeutic agents for different enzymes, contributing to the development of highly efficient inhibitors.

Crystal structures of human 17β‐hydroxysteroid dehydrogenase type 1 complexed with estrone and NADP+ reveal the mechanism of substrate inhibition

“…An inhibitor design, in the light of reversible binding of E1, was conducted by manual editing using seesar . The complex structures of 17β‐HSD1 with inhibitor CC‐156 , 2‐MeO‐CC‐156 and PBRM have showed a space in the active site which was not occupied by the native substrates and suitable to accommodate an extra benzylamide ring . Thus, we added a benzylamide ring moiety at the O‐3 of E1 to form a novel compound 3‐(((8 R ,9 S ,13 S ,14 S )‐13‐methyl‐17‐oxo‐7,8,9,11,12,13,14,15,16,17‐decahydro‐6 H ‐cyclopenta[ ɑ ]phenanthren‐3‐yl)oxy) benzamide (SX7) (Fig.…”

Emerging and Re-Emerging Warheads for Targeted Covalent Inhibitors: Applications in Medicinal Chemistry and Chemical Biology

“…21 As a result, covalent inhibition is timedependent and prolonged exposure leads to an increase in target occupancy. Consequently, K D , IC 50 , or EC 50 values are not the appropriate measures for comparing covalent ligands because they vary over time and do not reflect the relative contribution of K I and k inact to the observed overall effect. Notably, time-dependent inhibition can also result from other factors like compound aggregation or instability in buffer and time-dependence cannot be considered as an ultimate proof of covalent binding despite the presence of a reactive group.…”

“…Although we aimed to include all relevant and recent information, this work should rather be considered a (personally biased) perspective on interesting chemistry and current developments and not a comprehensive review of the field. This article covers literature published before July 2018, therefore interesting work which appeared during the revision of the manuscript (e.g., cysteinetargeted cyanamides as Janus kinase 3 inhibitors, 49 histidinetargeted linear alkyl bromides as 17β-hydroxysteroid dehydrogenase inhibitors, 50 and methionine-targeted epoxides as bromodomain inhibitors 51 ), is not discussed. The article is organized by reactive amino acid side chains.…”

Cov_FB3D: A De Novo Covalent Drug Design Protocol Integrating the BA-SAMP Strategy and Machine-Learning-Based Synthetic Tractability Evaluation

“…For example, ibrutinib , afatinib , , and osimertinib can covalently react with cysteine, the inhibitors reported by Dalton et al and Mukherjee et al can form covalent bonds with lysine. In addition, some other residues, such as serine, , threonine, tyrosine, methionine, histidine, and glutamate, can also form covalent bonds with inhibitors …”

“…For example, ibrutinib 9,10 afatinib, 11,12 and osimertinib 13 can covalently react with cysteine, the inhibitors reported by Dalton et al 14 and Mukherjee et al 15 can form covalent bonds with lysine. In addition, some other residues, such as serine, 16,17 threonine, tyrosine, 18 methionine, 19 histidine, 20 and glutamate, 21 can also form covalent bonds with inhibitors. 22 The increased interest in covalent drug discovery has led to the development of computational tools for designing and characterizing novel covalent inhibitors.…”