Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors

• Published in: Journal of medicinal chemistry Vol. 59; no. 7; pp. 3272 - 3302
• Main Authors: Kavanagh, Madeline E, Coyne, Anthony G, McLean, Kirsty J, James, Guy G, Levy, Colin W, Marino, Leonardo B, de Carvalho, Luiz Pedro S, Chan, Daniel S. H, Hudson, Sean A, Surade, Sachin, Leys, David, Munro, Andrew W, Abell, Chris
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 14.04.2016; Amer Chemical Soc
• Subjects: Bacterial Proteins - antagonists & inhibitors; Binding Sites; Chemistry, Medicinal; Crystallography, X-Ray; Cytochrome P-450 Enzyme System - chemistry; Drug Design; Enzyme Inhibitors - chemistry; Enzyme Inhibitors - pharmacology; Humans; Life Sciences & Biomedicine; Ligands; Mycobacterium tuberculosis; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - enzymology; Pharmacology & Pharmacy; Protein Binding; Protein Structure, Tertiary; Science & Technology; Tuberculosis - drug therapy; Tuberculosis - microbiology; BIOPHYSICAL CHARACTERIZATION; MURINE TUBERCULOSIS; LIGAND EFFICIENCY; ACTIVE-SITE; TRYPANOSOMA-CRUZI; DRUG DISCOVERY; CYTOCHROME-P450 CYP121; AZOLE DRUGS; 4-AMINOPYRIDYL-BASED INHIBITORS; BINDING
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/acs.jmedchem.6b00007

The essential enzyme CYP121 is a target for drug development against antibiotic resistant strains of Mycobacterium tuberculosis. A triazol-1-yl phenol fragment 1 was identified to bind to CYP121 using a cascade of biophysical assays. Synthetic merging and optimization of 1 produced a 100-fold improvement in binding affinity, yielding lead compound 2 (K D = 15 μM). Deconstruction of 2 into its component retrofragments allowed the group efficiency of structural motifs to be assessed, the identification of more LE scaffolds for optimization and highlighted binding affinity hotspots. Structure-guided addition of a metal-binding pharmacophore onto LE retrofragment scaffolds produced low nanomolar (K D = 15 nM) CYP121 ligands. Elaboration of these compounds to target binding hotspots in the distal active site afforded compounds with excellent selectivity against human drug-metabolizing P450s. Analysis of the factors governing ligand potency and selectivity using X-ray crystallography, UV–vis spectroscopy, and native mass spectrometry provides insight for subsequent drug development.