menaquinone-9

Abstract

Cytochrome P450 monooxygenases (CYPs/P450s) are well known for their role in organisms’ primary and secondary metabolism. Among 20 P450s of the tuberculosis-causing Mycobacterium tuberculosis H37Rv, CYP128A1 is particularly important owing to its involvement in synthesizing electron transport molecules such as menaquinone-9 (MK9). This study employs different in silico approaches to understand CYP128 P450 family’s distribution and structural aspects. Genome data-mining of 4250 mycobacterial species has revealed the presence of 2674 CYP128 P450s in 2646 mycobacterial species belonging to six different categories. Contrast features were observed in the CYP128 gene distribution, subfamily patterns, and characteristics of the secondary metabolite biosynthetic gene cluster (BGCs) between M. tuberculosis complex (MTBC) and other mycobacterial category species. In all MTBC species (except one) CYP128 P450s belong to subfamily A, whereas subfamily B is predominant in another four mycobacterial category species. Of CYP128 P450s, 78% was a part of BGCs with CYP124A1, or together with CYP124A1 and CYP121A1. The CYP128 family ranked fifth in the conservation ranking. Unique amino acid patterns are present at the EXXR and CXG motifs. Molecular dynamic simulation studies indicate that the CYP128A1 bind to MK9 with the highest affinity compared to the azole drugs analyzed. This study provides comprehensive comparative analysis and structural insights of CYP128A1 in M. tuberculosis.

2.6. CYP128A1 Protein Model Has High Affinity to Menaquinone-9

In P450 enzyme systems, substrates and azole drugs are known to coordinate with the ferric core of the heme group. In the case of MK9, coordination takes place at the end of its hydrophobic tail, consistent with omega hydroxylation of the molecule [,]. For azole drugs, coordination occurs via the imidazole ring. Importantly, docking of MK9 and azole drugs was performed in a non-covalent way in the present paper. Therefore, no coordination was predicted for the tested ligands, which would require more thorough investigation, especially considering changes in electronic density. However, since non-covalent binding is a critical step in the establishment of covalent interactions, we believe the present results still provide a good indication of how azoles drugs can interact with CYP128A1 and how they rank in terms of affinity.

3.11. Redocking of Compounds

MK9 and the azoles compounds were re-docked on their corresponding set of equilibrated structures using the MOE’s dock (six structures for MK9, 10 structures for each of the azole drugs). The same options as in the first docking step were used (see ).