Structural Elucidation and Molecular Docking of a Novel Antibiotic Compound from Cyanobacterium Nostoc sp. MGL001

Abstract

Cyanobacteria are rich source of array of bioactive compounds. The present study reports a novel antibacterial bioactive compound purified from cyanobacterium Nostoc sp. MGL001 using various chromatographic techniques viz. thin layer chromatography (TLC) and high performance liquid chromatography (HPLC). Further characterization was done using electrospray ionization mass spectroscopy (ESIMS) and nuclear magnetic resonance (NMR) and predicted structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy) -5, 8, 13, 16-tetraaza-hexacene - 2, 3 dicarboxylic acid (EMTAHDCA). Structure of EMTAHDCA clearly indicated that it is a novel compound that was not reported in literature or natural product database. The compound exhibited growth inhibiting effects mainly against the gram negative bacterial strains and produced maximum zone of inhibition at 150 μg/mL concentration. The compound was evaluated through in silico studies for its ability to bind 30S ribosomal fragment (PDB ID: 1YRJ, 1MWL, 1J7T, and 1LC4) and OmpF porin protein (4GCP, 4GCQ, and 4GCS) which are the common targets of various antibiotic drugs. Comparative molecular docking study revealed that EMTAHDCA has strong binding affinity for these selected targets in comparison to a number of most commonly used antibiotics. The ability of EMTAHDCA to bind the active sites on the proteins and 30S ribosomal fragments where the antibiotic drugs generally bind indicated that it is functionally similar to the commercially available drugs.

Keywords: Nostoc sp. MGL001; OmpF porin protein; RNA fragments; antibacterial agent; molecular docking; novel bioactive compound.

Figure 1

Microphotographs of Nostoc sp. MGL001. (A) and (B) showing filament with vegetative cell (VC) and heterocysts (H).

Figure 2

Neighbor-joining tree of Nostoc sp MGL001 with reference strains using 16S rDNA gene sequences. Bootstrap values (%) are based on 1000 replicates and shown at the branch point with more than 50% bootstrap values. ♦ Representing the cyanobacteriaum Nostoc sp. MGL001 used in the present study.

Figure 3

TLC pattern of methanolic crude extract from Nostoc sp. MGL001 (A) using carbon tetrachloride and methanol (9:1) as mobile solvent. (B) TLC pattern of 2nd TLC spot using ethyl acetate and hexane (1:1) as mobile solvent.

Figure 4

HPLC chromatogram of the spot “E” fraction of the Nostoc sp. MGL001 crude extract obtained from TLC.

Figure 5

¹H NMR spectrum of the bioactive compound (spot “E” eluate) derived from Nostoc sp. MGL001.

Figure 6

¹³C NMR spectrum of the bioactive compound (spot “E” eluate) derived from Nostoc sp. MGL001.

Figure 7

Proposed structure of bioactive compound was 9-Ethyliminomethyl-12-(morpholin - 4 - ylmethoxy) - 5, 8, 13, 16 - tetraaza - hexacene - 2, 3 dicarboxylicacid (EMTAHDCA).

Figure 8

In silico interaction between selected ligand (EMTAHDCA) and target RNA fragment (A) 1YRJ (B) 1MWL, (C) 1J7T, (D) 1LC4.

Figure 9

In silico interaction between selected ligand (EMTAHDCA) and target OmpF porin protein (4GCP). (A) Poses of docked complexes, green color in sphere indicates prominent active site where the ligand interacted, (B) 2D level interaction, (C) 3D level interaction.

Figure 10

In silico interaction between selected ligand (EMTAHDCA) and target OmpF porin protein (4GCQ). (A) Poses of docked complexes, green color in sphere indicates prominent active site where the ligand interacted, (B) 2D level interaction, (C) 3D level interaction.

Figure 11

In silico interaction between selected ligand (EMTAHDCA) and target OmpF porin protein (4GCS). (A) Poses of docked complexes, green color in sphere indicates prominent active site where the ligand interacted, (B) 2D level interaction, (C) 3D level interaction.

Figure 12

H-H COSY NMR spectrum of EMTAHDCA.

Figure 13

DEPT-135 NMR spectrum of EMTAHDCA.

Figure 14

DEPT-90 NMR spectrum of EMTAHDCA.