Determinants of the Inhibition of DprE1 and CYP2C9 by Antitubercular Thiophenes

Abstract

Mycobacterium tuberculosis (Mtb) DprE1, an essential isomerase for the biosynthesis of the mycobacterial cell wall, is a validated target for tuberculosis (TB) drug development. Here we report the X‐ray crystal structures of DprE1 and the DprE1 resistant mutant (Y314C) in complexes with TCA1 derivatives to elucidate the molecular basis of their inhibitory activities and an unconventional resistance mechanism, which enabled us to optimize the potency of the analogs. The selected lead compound showed excellent in vitro and in vivo activities, and low risk of toxicity profile except for the inhibition of CYP2C9. A crystal structure of CYP2C9 in complex with a TCA1 analog revealed the similar interaction patterns to the DprE1–TCA1 complex. Guided by the structures, an optimized molecule was generated with differential inhibitory activities against DprE1 and CYP2C9, which provides insights for development of a clinical candidate to treat TB.

Chalcone analogues: Synthesis, activity against Meloidogyne incognita, and in silico interaction with cytochrome P450

“…After the elimination of mutant enzymes, followed by reconstruction of missing amino acid residues and optimization of the three‐dimensional structure of the enzymes, only one CYP1A2 enzyme remained: 2hi4 (Sansen et al, ). After the same process, three CYP2C9 enzymes remained: 1r9o, 5k7k and 5w0c (Liu et al, ; Swain et al, ; Wester et al, ). For CYP2D6 and CYP3A4, no enzymes remained.…”

“…Affinities of (1 E ,4 E )‐1,5‐di(4‐nitrophenyl)‐2‐butylpenta‐1,4‐dien‐3‐one ( 6 ) and (2 E ,6 E )‐2,6‐dibenzylidenecyclohexanone (A2) for the cavity CAV‐1, localized on the surface of the cytochrome P450 1A2 2hi4 (Sansen et al, ), and affinities of 6 and (2 E ,6 E )‐2,6‐bis(4‐hydroxybenzylidene)cyclohexanone (A0) for the cavity CAV‐2 that is inside the cytochrome P450 2C9 1r9o, 5k7k and 5w0c (Liu et al, ; Swain et al, ; Wester et al, ). Calculations were done with Autodock Vina 1.1.2 and Autodock 4.2.6 (Morris et al, ; Trott & Olson, ).…”

“…The three‐dimensional structures were aligned to the optimized structure of the CYP1A2 2hi4 (Sansen et al, ) through Lovoalign 1.1.0 software (Martínez, Andreani, & Martínez, ), which also calculated the root‐mean‐square deviations (RMSD) between the remaining enzymes. Only the optimized three‐dimensional structures of one CYP1A2 (2hi4) (Sansen et al, ) and three CYP2C9 (1r9o, 5k7k, 5w0c) (Liu et al, ; Swain et al, ; Wester et al, ) were converted to the pdbqt format through AutodockTools 1.5.7rc1 software (Morris et al, ). In a similar way, the most stable conformations of A0 and A2, according to optimizations carried out with Mopac2016 as described above, were converted to the pdbqt format by AutodockTools 1.5.7rc1 (Morris et al, ).…”

Promiscuous Targets for Antitubercular Drug Discovery: The Paradigm of DprE1 and MmpL3

“…Currently, 33 DprE1 structures from M. tuberculosis or M. smegmatis have been deposited in the Protein Data Bank, as apoenzyme [41,53] or in complex with both covalent [41,43,44,49,54] and noncovalent inhibitors [43,50,[55][56][57][58]. The enzyme is characterized by the two-domain topology of the vanillyl-alcohol oxidase family of oxidoreductases, which includes a flavin adenine dinucleotide (FAD)-binding domain and the substrate-binding domain [41].…”

Redox‐guided small molecule antimycobacterials

“…Transcriptional analysis has shown that the genes involved in Mtb persistence are down‐regulated upon TCA1 treatment. Liu et al have further validated DprE1 as a target of TCA1 by reporting the X‐ray crystal structure of TCA1 complex with the enzyme . They have also showed that TCA1 does inhibit human CYP2C9, which may lead to its toxicity.…”