Cytochrome P450 CYP121A1 is a well-known drug target against Mycobacterium tuberculosis, the human pathogen that causes the deadly disease
tuberculosis (TB). CYP121A1 is a unique
P450 enzyme because it uses classical and non-classical P450 catalytic processes and has distinct structural features among P450s. However, a detailed investigation of CYP121A1
protein structures in terms of active site cavity dynamics and key
amino acids interacting with bound
ligands has yet to be undertaken. To address this research knowledge gap, 53 CYP121A1 crystal structures were investigated in this study. Critical
amino acids required for CYP121A1's overall activity were identified and highlighted this
enzyme's rigid architecture and substrate selectivity. The CYP121A1-fluconazole crystal structure revealed a novel
azole drug-P450 binding mode in which
azole heme coordination was facilitated by a water molecule. Fragment-based inhibitor approaches revealed that CYP121A1 can be inhibited by molecules that block the substrate channel or by directly interacting with the P450
heme. This study serves as a reference for the precise understanding of CYP121A1 interactions with different
ligands and the structure-function analysis of
P450 enzymes in general. Our findings provide critical information for the synthesis of more specific CYP121A1 inhibitors and their development as novel anti-TB drugs.