Identification of Morpholino Thiophenes as Novel Mycobacterium tuberculosis Inhibitors, Targeting QcrB

Abstract

With the emergence of multidrug-resistant strains of Mycobacterium tuberculosis there is a pressing need for new oral drugs with novel mechanisms of action. Herein, we describe the identification of a novel morpholino-thiophenes (MOT) series following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis strain H37Rv. The design, synthesis, and structure-activity relationships of a range of analogues around the confirmed actives are described. Optimized leads with potent whole cell activity against H37Rv, no cytotoxicity flags, and in vivo efficacy in an acute murine model of infection are described. Mode-of-action studies suggest that the novel scaffold targets QcrB, a subunit of the menaquinol cytochrome c oxidoreductase, part of the bc1-aa3-type cytochrome c oxidase complex that is responsible for driving oxygen-dependent respiration.

Figure 1

Antitubercular agents with a thiophene-2-carboxamide substructure.

Scheme 1. General Synthesis of Morpholino–Thiophines

Reagents and conditions: (i) Morpholine, DCM, 0 °C to rt; (ii) Lawesson’s reagent, 100 °C; (iii) 2-Bromoacetamide, NaH, THF, 0 °C to rt; (iv) DIAD, PPh₃, phenylethylalcohol (R₁OH), THF, rt.

Scheme 2. Alternative Synthesis of Morpholino–Thiophines

Reagents and conditions: (i) DIAD, PPh₃, phenylethylalcohol, THF, rt; (ii) Iodine, LDA, THF, −78 °C; (iii) CaCl₂, NH₃, MeOH, 150 °C, μW; (iv) Suzuki: Boronic acid, Cs₂CO₃, Pd(PPh₃)₄, DMF, 80 °C or Buchwald: Amine, Proline, CuI, K₃PO₄, DMSO, 80 °C, μW; (v) LDA, DMF, THF, −78 °C; (vi) Amine, NaBH(OAc)₃, CHCl₃, rt; (vii) O-tetrahydropyran-2-yl hydroxylamine, LiHDMS, THF, −78 °C; (viii) p-toluenesulfonic acid monohydrate, MeOH.

Figure 2

Overlay of known QcrB inhibitor Q203 (green) with 37 (yellow). Further 2D comparison of QcrB pharmacophores is shown in the Supporting Information (Table 1).

Figure 3

ATP levels were measured in M. tuberculosis exposed to compounds for 24 h. Growth was monitored by OD₅₉₀: (A–D) MOT compounds, (E) Q203, and (F) Rifampicin. Results are representative of 2 independent experiments.