Exploring the plasticity of the InhA substrate-binding site using new diaryl ether inhibitors

[Display omitted] •Design and synthesis of new diaryl ether derivatives that target InhA.•Bis-diaryl ethers with improved activity against the enzyme.•Crystal structure of InhA-NAD+ in complex with the most potent compound.•Structural analysis revealed the protein adaptability to relatively large inhibitors.•Opening of the minor portal underlines molecular plasticity. Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains a worldwide scourge with more than 10 million people affected yearly. Among the proteins essential for the survival of Mtb, InhA has been and is still clinically validated as a therapeutic target. A new family of direct diaryl ether inhibitors, not requiring prior activation by the catalase peroxidase enzyme KatG, has been designed with the ambition of fully occupying the InhA substrate-binding site. Thus, eleven compounds, featuring three pharmacophores within the same molecule, were synthesized. One of them, 5-(((4-(2-hydroxyphenoxy)benzyl)(octyl)amino)methyl)-2-phenoxyphenol (compound 21), showed good inhibitory activity against InhA with IC50 of 0.70 µM. The crystal structure of compound 21 in complex with InhA/NAD+ showed how the molecule fills the substrate-binding site as well as the minor portal of InhA. This study represents a further step towards the design of new inhibitors of InhA.