Multifunctional in vitro, in silico and DFT analyses on antimicrobial BagremycinA biosynthesized by Micromonospora chokoriensis CR3 from Hieracium canadense

Abstract

Among the actinomycetes in the rare genera, Micromonospora is of great interest since it has been shown to produce novel therapeutic compounds. Particular emphasis is now on its isolation from plants since its population from soil has been extensively explored. The strain CR3 was isolated as an endophyte from the roots of Hieracium canadense, and it was identified as Micromonospora chokoriensis through 16S gene sequencing and phylogenetic analysis. The in-vitro analysis of its extract revealed it to be active against the clinical isolates of methicillin-resistant Staphylococcus aureus (MRSA) and Candida tropicalis (15 mm). No bioactivity was observed against Gram-negative bacteria, Escherichia coli ATCC 25922, and Klebsiella pneumoniae ATCC 706003. The Micromonospora chokoriensis CR3 extract was also analyzed through the HPLC-DAD-UV-VIS resident database, and it gave a maximum match factor of 997.334 with the specialized metabolite BagremycinA (BagA). The in-silico analysis indicated that BagA strongly interacted with the active site residues of the sterol 14-α demethylase and thymidylate kinase enzymes, with the lowest binding energies of - 9.7 and - 8.3 kcal/mol, respectively. Furthermore, the normal mode analysis indicated that the interaction between these proteins and BagA was stable. The DFT quantum chemical properties depicted BagA to be reasonably reactive with a HOMO-LUMO gap of (ΔE) of 4.390 eV. BagA also passed the drug-likeness test with a synthetic accessibility score of 2.06, whereas Protox-II classified it as a class V toxicity compound with high LD₅₀ of 2644 mg/kg. The current study reports an endophytic actinomycete, M. chokoriensis, associated with H. canadense producing the bioactive metabolite BagA with promising antimicrobial activity, which can be further modified and developed into a safe antimicrobial drug.

Figure 1

Neighbour Joining phylogenetic tree analysis of 16S rRNA gene sequence of Micromonospora chokoriensis CR3 and its twenty nearest homologues. Micromonospora chokoriensis CR3 clustered together with other Micromonospora sp. 16S rRNA gene sequences. 16S rRNA gene sequence of Luedemannella helvata was used as an out-group.

Figure 2

Total UV absorption spectra of Micromonospora chokoriensis CR3 at 230 (blue), 260 (red), 280 (light green), 360 (pink), 435 nm (green) wavelengths and an overlay of UV/Vis spectra match with NL 19KF (1) at 230 nm, retention time 3.59 min (blue = extract, red = database) and BagA (2) at 230, 280 nm, retention time 7.9 min (blue = extract, red = database).

Figure 3

Molecular Docking Analysis of CaCYP51 and hCYP51 with BagA (a) The 3D and 2D molecular docking interactions of CaCYP51-BagA complex. (b) The 3D and 2D molecular docking interactions of hCYP51-BagA complex.

Figure 4

Molecular Docking Analysis of SaTMK and hTMK with BagA (a) The 3D and 2D molecular docking interactions of SaTMK-BagA complex. (b) The 3D and 2D molecular docking interactions of hTMK-BagA complex.

Figure 5

MD Simulation: normal mode analysis of CaCYP51-BagA complex. (a) Deformability (b) B-factor (c) Variance (d) Eigenvalues (e) Co-variance plot (f) Elastic network model.

Figure 6

MD Simulation: normal mode analysis of SaTMK-BagA Complex. (a) Deformability (b). B-factor (c). Variance, (d). Eigenvalues (e). Co-variance plot (f). Elastic network model.

Figure 7

DFT Quantum Chemical Analysis of BagA (a) Frontier molecular orbital HOMO plot (b) Frontier molecular orbital LUMO plot. HOMO and LUMO plots are representing the positive (Pink) and negative (Cyan) phase distribution in molecular orbital wave function (c) Molecular electrostatic potential (MEP) plot showing the red (Electron rich) and blue (Electron poor) regions. The analysis was done with B3LYP/6-31G-d using Gaussian 09W software.