LC-MS Analysis and In Silico Docking Study of Myristica Sebifera 30C against Staphylococcus aureus Proteins

Abstract

Background The homoeopathic medicine contains various biomolecules/compounds that can be identified through several modern instruments. Computational screening is one of the most common methods used for predicting these drug compound interactions with target protein/ligand molecules of microbial structure to formulate drug design.

Objective This study aimed to explore the biological compounds present in Myristica sebifera 30C and predict its physical interaction with Staphylococcus aureus proteins through the molecular docking method.

Materials and Methods An analysis of the phytoconstituents of Myristica sebifera 30C was performed using the Agilent 1290 Infinity LC system coupled to Agilent 6545 Accurate Mass Quadrupole Time-of-Flight (QTOF) with Agilent Jet Stream thermal gradient technology followed by a detailed docking study. The two phytoconstituents of Myristica sebifera 30C having more than 80% score were docked against two target proteins of S. aureus, namely, PDB:3U2D and PDB:1T2P, and their binding potential was measured. The ligand with the lower glide docking score is considered to have the best binding affinity.

Results Myristica sebifera 30C contains 21 compounds and mainly 1H-indole-3-ethanamine, N-methyl, and (2R,3S,4S)-4-(1,3-benzodioxol-5-yl)-4-(3,4-dimethoxyphenyl)-2,3-dimethylbutan-1-ol as bioactive components of the drug. It also contains (2R,3S,4S)-4-(1,3-benzodioxol-5-yl)-4-(3,4-dimethoxyphenyl)-2,3-dimethylbutan-1-o1, which has a lower glide score of –9.29 kcal/mol against the target protein PDB:3U2D, considered the best binding affinity. The amino acids involved in interaction between two biomolecules are ILEB:86, PROB:87, ILEB:51, ILEB:175, LEUB:103, and VALB:79.

Conclusion Based on the outcomes of the computational molecular docking analysis, it was concluded that bioactive substances found in Myristica sebifera 30C exhibit significant binding against DNA gyrase protein (PDB:3U2D) and Sortase A (PDB:1T2P) of S. aureus, which suggests that these substances may act as a promising antimicrobial agent.

Keywords

homeopathy - Myristica sebifera - phytocompound - molecular docking - computational screening - Staphylococcus aureus

Publication History

Article published online:
08 January 2025

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