Sulfur(vi) fluoride exchange as a key reaction for synthesizing biaryl sulfate core derivatives as potent hepatitis C virus NS5A inhibitors and their structure-activity relationship studies

Abstract

Extremely potent, new hepatitis C virus (HCV) nonstructural 5A (NS5A) featuring substituted biaryl sulfate core structures was designed and synthesized. Based on the previously reported novel HCV NS5A inhibitors featuring biaryl sulfate core structures which exhibit two-digit picomolar half-maximal effective concentration (EC₅₀) values against HCV genotype 1b and 2a, the new inhibitors equipped with the sulfate core structures containing diversely substituted aryl groups were explored. In this study, highly efficient, chemoselective coupling reactions between an arylsulfonyl fluoride and an aryl silyl ether, known as the sulfur(vi) fluoride exchange (SuFEx) reaction, were utilized. Among the inhibitors prepared based on the SuFEx chemistry, compounds 14, 15 and 29 exhibited two-digit picomolar EC₅₀ values against GT-1b and single digit or sub nanomolar activities against the HCV GT-2a strain. Nonsymmetrical inhibitors containing an imidazole and amide moieties on each side of the sulfate core structures were also synthesized. In addition, a biotinylated probe targeting NS5A protein was prepared for labeling using the same synthetic methodology.

Fig. 1. Discovery of biaryl sulfate derivatives as potent HCV NS5A inhibitors.

Fig. 2. Biaryl sulfate core based nonstructural 5A (NS5A) inhibitors and modification using sulfur(vi) fluoride exchange (SuFEx) chemistry.

Scheme 1. Synthesis of intermediates; reagents and conditions: (a) Pd/C, H₂, MeOH, room temperature (rt), 24 h, 99%; (b) EDCI, N-Boc-l-proline, CH₂Cl₂, rt, 4 h, 59–96%; (c) CuBr₂, EA/CHCl₃, reflux, 8 h, 81%; (d) N-Boc-l-proline, N,N-diisopropylethylamine (DIPEA), acetonitrile, rt, 5 h, 72–91%; (e) NH₄OAc, toluene, 95 °C, 20 h, 45–52%.

Scheme 2. Synthesis of 3-(2-((S)-1-((methoxycarbonyl)-l-valyl)pyrrolidin-2-yl)-1H-imidazol-5-yl)phenyl(3-((S)-1-((R)-2-((methoxycarbonyl)amino)-2-phenylacetyl)pyrrolidine-2-carboxamido)phenyl) sulfate.

Scheme 3. (a) TBDMSCl, Imidazole, CH₂Cl₂, rt, 4 h, 81%; (b) DBU, DMF, 50 °C, 12 h, 75%; (c) TFA, CH₂Cl₂, rt, 30 m; (d) EDCI, HOBt, DIPEA, Biotin, CH₂Cl₂, rt, 16 h, 96%.

Fig. 3. Docking of (A) BMK-21007, (B) BMK-21014, and (C) 11 to an NS5A (3FQQ) dimer model. For clarity purpose, only residues having interactions were shown. BMK-21007, BMK-21014, and 11 are shown in stick and surrounding residues were shown in line. Various interactions are shown in dashes. (For more clarity see the ESI, Fig. S4†). (D) Superposed model of inhibitors inside 3FQQ dimer model. BMK-21007, BMK-21014, and 11 are shown blue, green and red, respectively.