Hepatitis C Virus NS3/4A Protease Inhibitors Incorporating Flexible P2 Quinoxalines Target Drug Resistant Viral Variants

Abstract

A substrate envelope-guided design strategy is reported for improving the resistance profile of HCV NS3/4A protease inhibitors. Analogues of 5172-mcP1P3 were designed by incorporating diverse quinoxalines at the P2 position that predominantly interact with the invariant catalytic triad of the protease. Exploration of structure-activity relationships showed that inhibitors with small hydrophobic substituents at the 3-position of P2 quinoxaline maintain better potency against drug resistant variants, likely due to reduced interactions with residues in the S2 subsite. In contrast, inhibitors with larger groups at this position were highly susceptible to mutations at Arg155, Ala156 and Asp168. Excitingly, several inhibitors exhibited exceptional potency profiles with EC50 values ≤ 5 nM against major drug resistant HCV variants. These findings support that inhibitors designed to interact with evolutionarily constrained regions of the protease, while avoiding interactions with residues not essential for substrate recognition, are less likely to be susceptible to drug resistance.

Avoiding Drug Resistance by Substrate Envelope-Guided Design: Toward Potent and Robust HCV NS3/4A Protease Inhibitors

“…S1), and we have previously shown that inhibitors must fit within the envelope to have a flat profile against resistance (37)(38)(39). Relocating the macrocyle to fit within the substrate envelope in 5172-mcP1P3 (35) and the closely related parent compound (35) (Fig. 1) indeed achieved a flatter resistance profile than that of grazoprevir but unfortunately resulted in potency loss against the WT protease in enzymatic assays.…”

“…The resulting inhibitor, 5172-mcP1P3, was less susceptible to single-site RASs, particularly A156T (29), and the crystal structures validated that the binding mode of the P2 quinoxaline moiety stacking against catalytic residues was retained (31). Further optimization by modifications at the 3-position of the P2 quinoxaline moiety to decrease interactions with the S2 subsite residues Arg155 and Ala 156 revealed that compounds with a smaller methyl group at this position retains better activity against resistant variants (35). The resulting inhibitor ( Fig.…”

“…This design strategy involves decreasing interactions with variable residues that mutate to confer resistance (while keeping interactions with the invariable catalytic triad) and optimally filling the active-site pockets. We rationally designed HCV protease inhibitors that retain potency Change of the macrocycle location (5172-mcP1P3) and optimization of the P2 quinoxaline moiety led to the parent compound (35) modified in this study. The canonical nomenclature for drug moiety positioning and the P4 moiety altered are indicated.…”

Bulky Diamine Ligand Promotes Cross‐Coupling of Difluoroalkyl Bromides by Iron Catalysis

“…[2] Most of these well-developed methods are focused on copper-, [2,3] palladium-, [2,4] and nickel-catalyzed fluoroalkylations, [2,5] while the use of inexpensive,n ontoxic and environmentally benign transition metals,s uch as iron, as ac atalyst remains appealing.F or instance,although the iron-catalyzed Kumada reactions have been well established since Kochisp ioneering work, [6,7] the iron-catalyzed fluoroalkylations between Grignard reagents and fluoroalkyl halides has not been reported thus far because traditional catalytic systems often lead to defluorination reactions. [9] Inspired by the previous work on iron/TMEDA( L1) catalyzed cross-couplings between Grignard reagents and alkyl halides, [10] we initially focused our efforts on the crosscoupling of phenyl magnesium bromide (1a)w ith the unactivated difluoroalkyl bromide 2a in the presence of FeCl 3 (10 mol %) with TMEDA( L1;1 0mol %) as al igand (Scheme 1a). [9] Inspired by the previous work on iron/TMEDA( L1) catalyzed cross-couplings between Grignard reagents and alkyl halides, [10] we initially focused our efforts on the crosscoupling of phenyl magnesium bromide (1a)w ith the unactivated difluoroalkyl bromide 2a in the presence of FeCl 3 (10 mol %) with TMEDA( L1;1 0mol %) as al igand (Scheme 1a).…”

Bulky Diamine Ligand Promotes Cross‐Coupling of Difluoroalkyl Bromides by Iron Catalysis

“…[8] Herein, we report the first example of ironcatalyzed difluoroalkylation of arylmagnesiums with difluoroalkyl bromides.T he approach allows av ariety of difluoroalkyl bromides,i ncluding gaseous bromodifluoromethane, and provides ag eneral and cost-efficient method to difluoroalkylated arenes,adistinct class of fluorinated compounds found in many biologically active molecules. [9] Inspired by the previous work on iron/TMEDA( L1) catalyzed cross-couplings between Grignard reagents and alkyl halides, [10] we initially focused our efforts on the crosscoupling of phenyl magnesium bromide (1a)w ith the unactivated difluoroalkyl bromide 2a in the presence of FeCl 3 (10 mol %) with TMEDA( L1;1 0mol %) as al igand (Scheme 1a). However, the desired difluoroalkylated arene 3a was not obtained because of the severe defluorination of 2a.T he slow addition of 1a to the reaction system showed abeneficial effect, but only 20 %yield of 3awas obtained and the defluorination reactions remained al arge hurdle.T o address this crucial issue,asuitable catalytic iron system is essential.…”