Targeting Mycobacterium tuberculosis: Design and synthesis of CYP121A1 inhibitors

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Date
2024-01-24
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Cardiff University
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb), which continues to be a highly lethal disease owing to the drug resistance crisis. Drug resistant strains of Mtb represent a major therapeutic challenge, so new anti-tuberculosis agents are desperately needed. Among 20 Mtb cytochrome P450 enzymes, CYP121A1 was found to be a target of interest owing to its importance for Mtb cell viability and its high affinity to azole antifungal drugs. The aim of this project was to design and develop novel CYP121A1 inhibitors for treatment of TB with both optimum binding and antimycobacterial activity. In the present work, docking studies using MOE and MD simulations using the Desmond programme of Schrödinger software were used in designing different series of potential CYP121A1 inhibitors that mimicked the binding pattern of the CYP121A1 natural substrate, the cyclodipeptide dicyclotyrosine (cYY). Different scaffolds were used in the design: diaryl pyrazoles (Chapter 2), benzoxazoles (Chapter 3), chroman-4-ones (Chapter 4) and tetralones (Chapter 5), and various potential haem binding groups were incorporated including imidazole, triazole, tetrazole and pyridine. The designed ligand structures showed a consistent binding mode in a region of the active site located between the haem iron and the expected access channel, between the F and G α-helices, in a position comparable with cYY in CYP121A1. A synthetic scheme for each series was developed after several optimisation trials. Final products were obtained with varying yields followed by structural characterisation using NMR (1H, 19F and 13C) along with purity analysis using HPLC-MS and/or elemental analysis. All final compounds were evaluated against Mtb H37Rv (MIC90) and compared with the reference compounds: rifampicin, isoniazid, and kanamycin. The most promising series were screened against resistant Mtb strains. CYP121A1 binding affinity studies (KD) were performed using UV-Vis spectral absorption and compared with cYY. Protein-detected 1D 19F NMR spectroscopy was conducted as an additional binding test and cYY was used as a reference standard. The chroman-4-one and tetralone series were the most promising scaffolds followed by the pyrazole series, whereas the benzoxazole series was inactive. This research led to an effective design and synthesis of CYP121A1 inhibitors, which demonstrated good antimycobacterial activity against Mtb susceptible and resistant strains with optimal binding affinity.
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Keywords
Tuberculosis, Mycobacterium tuberculosis, CYP121A1, Drug Design, Drug Synthesis, cYY
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