Design, synthesis, in silico and in vitro evaluation of novel diphenyl ether derivatives as potential antitubercular agents

Abstract

Diphenyl ether derivatives inhibit mycobacterial cell wall synthesis by inhibiting an enzyme, enoyl-acyl carrier protein reductase (InhA), which catalyses the last step in the fatty acid synthesis cycle of genus Mycobacterium. To select and validate a protein crystal structure of enoyl-acyl carrier protein reductase of Mycobacterium tuberculosis for designing inhibitors using molecular modelling, a cross-docking and correlation study was performed. A series of novel 1-(3-(3-hydroxy-4-phenoxyphenyl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl) ethan-1-ones were synthesized from this model and screened for their antitubercular activity against M. tuberculosis H37Rv. Compound PYN-8 showed good antitubercular activity on M. tuberculosis H37Rv (MIC = 4-7 µM) and Mycobacterium bovis (% inhibition at 10 µM = 95.91%). Cytotoxicity of all the synthesized derivatives was assessed using various cell lines, and they were found to be safe. Structure of PYN-8 was also confirmed by single-crystal X-ray diffraction. The molecular modelling studies also corroborated the biological activity of the compounds. Further, in silico findings revealed that all these tested compounds exhibited good ADME properties and drug likeness and thus may be considered as potential candidates for further drug development.

Keywords: Antitubercular; Correlation study; Diphenylether; InhA; Molecular docking; TB.

Figure 1.

Design strategy and active site of InhA showing diphenyl ether derivative substituted at 5^th chlorine position protruding into the isonicotinoyl binding pocket containing InhA complexes of isoniazid (red colour) and ethionamide (yellow colour)

Figure 2.

Binding free energy vs pIC₅₀ correlation graph with correlation value R²

Figure 3.

Induced fit docked pose of PYN-8 on 3FNE

Figure 4.

Induced fit docked pose of Triclosan on 3FNE

Figure 5.

Water map of 3FNE protein showing PYN-8 displacing water site number 68

Figure 6.

ORTEP diagram of PYN-8. Displacement ellipsoids are drawn at the 30% probability level.

Figure 8.

All 11 crystal structures aligned over 2X23 crystal structure

Figure 9.

All the extracted ligands aligned using flexible ligand alignment

Scheme 1.. Synthesis of pyrazoline derivatives of diphenyl ethers (PYN series)

1) Phenyl boronic acid 2) 3-hydroxy-4-phenoxy 3) 1-(3-methoxy-4-phenoxyphenyl)ethan-1-one 4) 1-(3-hydroxy-4-phenoxyphenyl)ethan-1-one 5) (E)-1-(3-hydroxy-4-phenoxyphenyl)-3-phenylprop-2-en-1-one 6) 1-(3-(3-hydroxy-4-phenoxyphenyl)-5-phenyl-4,5-dihydro-1H-pyrazol-1-yl)ethan-1-one acetophenone a) Copper acetate monohydrate, Pyridine, anhydrous dichloromethane, 4Å Molecular Sieves b) BBr₃, anhydrous dichloromethane, −78°C c) Substituted benzaldehydes, LiOH.H₂O, Ethanol d) Hydrazine hydrate, Glacial acetic acid