GC-MS analysis of phytoconstituents from Amomum nilgiricum and molecular docking interactions of bioactive serverogenin acetate with target proteins

Abstract

Amomum nilgiricum is one of the plant species reported from Western Ghats of India, belonging to the family Zingiberaceae, with ethno-botanical values, and is well-known for their ethno medicinal applications. In the present investigation, ethyl acetate and methanol extracts of A. nilgiricum were analyzed by Fourier transform infrared spectrometer (FTIR) and gas chromatography-mass spectrometry (GC-MS) to identify the important functional groups and phytochemical constituents. The FTIR spectra revealed the occurrence of functional characteristic peaks of aromatic amines, carboxylic acids, ketones, phenols and alkyl halides group from leaf and rhizome extracts. The GC-MS analysis of ethyl acetate and methanol extracts from leaves, and methanol extract from rhizomes of A. nilgiricum detected the presence of 25 phytochemical compounds. Further, the leaf and rhizome extracts of A. nilgiricum showed remarkable antibacterial and antifungal activities at 100 mg/mL. The results of DPPH and ferric reducing antioxidant power assay recorded maximum antioxidant activity in A. nilgiricum methanolic leaf extract. While, ethyl acetate leaf extract exhibited maximum α-amylase inhibition activity, followed by methanolic leaf extract exhibiting aldose reductase inhibition. Subsequently, these 25 identified compounds were analyzed for their bioactivity through in silico molecular docking studies. Results revealed that among the phytochemical compounds identified, serverogenin acetate might have maximum antibacterial, antifungal, antiviral, antioxidant and antidiabetic properties followed by 2,4-dimethyl-1,3-dioxane and (1,3-¹³C₂)propanedioic acid. To our best knowledge, this is the first description on the phytochemical constituents of the leaves and rhizomes of A. nilgiricum, which show pharmacological significance, as there has been no literature available yet on GC-MS and phytochemical studies of this plant species. The in silico molecular docking of serverogenin acetate was also performed to confirm its broad spectrum activities based on the binding interactions with the antibacterial, antifungal, antiviral, antioxidant and antidiabetic target proteins. The results of the present study will create a way for the invention of herbal medicines for several ailments by using A. nilgiricum plants, which may lead to the development of novel drugs.

Figure 1

(a) FTIR spectrum from methanolic leaf extract of Amomum nilgiricum. (b) FTIR spectrum from ethyl acetate leaf extract of Amomum nilgiricum. (c) FTIR spectrum from methanolic rhizome extract of Amomum nilgiricum.

Figure 2

(a) Phytoconstituents detected in the methanol leaf extract of Amomum nilgiricum using gas chromatography-mass spectrometry. (b). chemical structure of nine phytocompounds identified based on the retention time and peak area, namely (1) 5-aminooxypentanoic acid (20.986 retention time and 4.082% peak area), (2) 3,7,9-trioxatricyclo[4.2.1.0^2,4]nonane (21.916 retention time and 19.379% peak area), (3) 1-(2,4,4-trimethylpentan-2-yl)-4-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]benzene (27.368 retention time and 3.129% peak area), (4) trimethyl-(2-trimethylsilylphenyl)silane (27.753 retention time and 3.171% peak area), (5) 3,5-bis(trimethylsilyl)cyclohepta-2,4,6-trien-1-one, (27.898 retention time and 4.369% peak area), (6) trimethyl-[4-[2-methyl-4-(4-trimethylsilyloxyphenyl)pent-4-en-2-yl]phenoxy]silane (28.043 retention time and 38.631% peak area), (7) trimethyl-[4-[4-(4-trimethylsilyloxyphenyl)hexan-3- (28.288 retention time and 16.246% peak area), (8) trimethyl-[[4-(trimethylsilylmethyl)phenyl]methyl]silane (28.489 retention time and 6.405% peak area) and (9) 1,1,1,3,5,5,5-heptamethyltrisiloxane (28.589 retention time and 4.588% peak area).

Figure 3

(a). Phytoconstituents detected in the ethyl acetate extract from Amomum nilgiricum leaves using gas chromatography-mass spectrometry. (b). Chemical structure of six phytocompounds identified based on the retention time and peak area, namely (1) octadec-1-yne, (19.950 retention time and 2.852% peak area), (2) 3,4-heptadien-2-one, 3-cyclopentyl-6-methyl- (21.086 retention time and 3.027% peak area), (3) [3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate (21.891 retention time and 82.105% peak area), (4) trimethyl-[4-(2,4,4-trimethylpentan-2-yl)phenoxy]silane (27.098 retention time and 3.757% peak area), (5) trimethyl-(2-trimethylsilylphenyl)silane (27.718 retention time and 4.706% peak area) and (6) 3,5-bis(trimethylsilyl)cyclohepta-2,4,6-trien-1-one (27.783 retention time and 3.553% peak area).

Figure 4

(a). Phytoconstituents detected in the methanol rhizome extract of Amomum nilgiricum using gas chromatography-mass spectrometry. (b). Chemical structure of ten phytocompounds identified based on the retention time and peak area, namely (1) ethyl 2-oxopropanoate (4.759 retention time and 2.271% peak area), (2) (1,3-¹³C₂)propanedioic acid (7.880 retention time and 6.142% peak area), (3) 2-butyl-4-[(E)-pentadec-4-enyl]-1,3,2-dioxaborinan-5-amine (15.473 retention time and 18.518% peak area), (4) 2,4-dimethyl-1,3-dioxane (16.399 retention time and 12.222% peak area), (5) 5-amino-6-nitroso-1H-pyrimidine-2,4-dione (16.989 retention time and 9.325% peak area), (6) (2R,4S,5S,6R)-3,8,9-trioxatricyclo[4.2.1.0^2,4]nonan-5-ol (18.084 retention time and 33.323% peak area), (7) (1R,2S,4R,5R)-3,7,9-trioxatricyclo[4.2.1.0^2,4]nonan-5-ol (18.635 retention time and 3.300% peak area), (8) (2S,4S,5R,6R)-3,8,9-trioxatricyclo[4.2.1.0^2,4]nonan-5-ol (18.755 retention time and 9.621% peak area), (9) 5-methylhex-3-yn-2-ol (19.430 retention time and 2.818% peak area) and (10) trimethylsilyl tetracosanoate (21.911 retention time and 2.460% peak area).

Figure 5

Antibacterial activity of leaf and rhizome extracts of A. nilgiricum at 25, 50 and 100 mg/ mL (a) Zone of inhibition from ethyl acetate leaf extract against Pseudomonas aeruginosa (b) Zone was from methanol leaf extract against Pseudomonas aeruginosa. (c) Zone of inhibition from ethyl acetate leaf extract against R. solanacearum (d) Zone of inhibition from methanolic rhizome extract against Ralstonia solanacearum. PC: Streptomycin (positive control); NC: solvent extract (negative control).

Figure 6

Antifungal activity of Amomum nilgiricum leaf and rhizome extracts at 25, 50 and 100 mg/mL (a) Zone of inhibition from ethyl acetate leaf extract against Alternaria alternata (b) methanol leaf extract against Alternaria alternata. (c) Ethyl acetate leaf extract against Pyricularia oryzae. (d) Methanolic rhizome extract against Pyricularia oryzae. PC: (Positive control) Nystatin; NC: Negative control (solvent).

Figure 7

Antioxidant activity of Amomum nilgiricum leaf and rhizome extracts. (a) DPPH radical scavenging activity. (b) Ferric reducing antioxidant power scavenging activity.

Figure 8

Antidiabetic enzymes activities of Amomum nilgiricum leaf and rhizome extracts. (a) α—amylase inhibition activity. (b) α—glucosidase inhibition activity. (c) aldose reductase inhibition activity.

Figure 9

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with bacterial target protein (5iwm) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by O26 in GLY341 (black arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the bacterial target protein. (c) Binding pose of the bacterial target protein with serverogenin acetate compound.

Figure 10

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with fungal target protein (4i9p) based on the binding energy generated by AutoDock program. (a) Hydrogen-bond interaction are formed by THR170 (blue arrow), ARG173 (red arrow), SER504 (green arrow), LYS503 (yellow arrow), HIS502 and HIS469 (pink arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the fungal target protein. (c) Binding pose of fungal target protein with serverogenin acetate compound.

Figure 11

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with viral target protein (1rev) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by GLN91 (orange arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the viral target protein. (c) Binding pose of viral target protein with serverogenin acetate compound.

Figure 12

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with antioxidant target protein (2he3) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by O in ARG146, ARG147 and ARG148 (red arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the anti-oxidant target protein. (c) Binding pose of antioxidant target protein with serverogenin acetate compound.

Figure 13

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with aldose reductase target protein (4ysl) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by O3 and OG in SER302 (green arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the aldose reductase target protein. (c) Binding pose of aldose reductase target protein with serverogenin acetate compound.

Figure 14

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with α-glucosidase target protein (5nn3) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by O3 in ALA284 (bright green arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the α-glucosidase target protein. (c) Binding pose of α-glucosidase target protein with serverogenin acetate compound.

Figure 15

In silico molecular docking shows the binding interaction of serverogenin acetate ([3,12-diacetyloxy-10,14-dimethyl-13-oxo-15-(5-oxo-2H-furan-3-yl)-2-oxapentacyclo[9.7.0.01,3.05,10.014,18]octadecan-7-yl] acetate) compound with α-amylase target protein (i-tasser) based on the binding energy generated by AutoDock program. (a) A hydrogen-bond interaction is formed by O26 in HE2, O27 in HE1, O34 in HE2, TRP59 (grey arrow), GLN63 (orange arrow), HIS305 (pink arrow) and ASP356 (purple arrow) in the serverogenin acetate compound. (b) A close-up view of serverogenin acetate compound that binds to the α-amylase target protein. (c) Binding pose of α-amylase target protein with serverogenin acetate compound.