Coumarin and fatty alcohol from root bark of strychnos innocua (delile): isolation, characterization and in silico molecular docking studies

Coumarin and fatty alcohol are abundant in nature, particularly in plants, and have been reported to have therapeutic uses. Strychnos innocua (Loganiaceae family) is commonly utilized for medicinal purposes in several African countries. Ethyl acetate extract of the plant (root bark) was subjected to chromatography separation, leading to the isolation of Umbelliferone (1) and 2,13-octadecadien-1-ol (2). Their structures were verified using mass spectrometry (MS) and nuclear magnetic resonance (NMR) and then compared with published data. This is the first time these compounds (1 and 2) have been isolated from S. innocua root bark. In the molecular docking analysis, the binding scores of the compounds (1 and 2) with the binding sites of Staphylococcus aureus pyruvate carboxylase (PDB: 3HO8) and Pseudomonas aeruginosa virulence factor regulator (PDB: 2OZ6) were − 5.6 and − 4.7 kcal/mol, and − 6.9 and − 5.7 kcal/mol, respectively. These were compared with ciprofloxacin (standard drug), which had docking scores of -6.6 and -8.7 kcal/mol, respectively. In conclusion, this study established the rich presence of Umbelliferone and 2,13-octadecadien-1-ol in the plant root bark, and their docking studies revealed moderate binding potential with the binding sites of S. aureus and P. aeruginosa.

Page 2 of 12 Uttu et al. Bulletin of the National Research Centre (2022) 46:174 Background Compounds isolated from plants have enormous potential in the development of new drugs (Sasidharan et al. 2011). In general, plants can be found all over the world, and their parts (leaves, stems, roots, fruit, and flowers) are employed in a variety of uses, including medicine (Umaru et al. 2019).
The phytochemical composition and secondary metabolites of plants such as coumarin and fatty alcohols contain active therapeutic components and are associated  with their pharmacological potential (Mondal et al. 2019;Uttu et al. 2022). Umbelliferone (7-hydroxycoumarin) is sometimes utilized as a fluorophore. It has a large π-π conjugated system that allows it to be used as a fluorescent sensor for a variety of biological applications (Raunio et al. 2020), such as antidiarrheal, antiulcerogenic, antibacterial, mutagenic, and antioxidant activities (Cruz and de-Figueriredo G. F., Pedro L. P., Amorin Y. M., Andrade J. T., Passos T. F. and Araujo M. G. D. 2020), whereas 2,13-octadecadien-1-ol was identified as one of the major phytochemical compounds in Epipremnum aureum and possesses diuretic, antimicrobial, antiulcer, anti-inflammatory, antioxidant, and pesticide activities (Meshram et al. 2016). The antimicrobial potential of natural compounds from plant origins has been assessed using a variety of in vitro, in vivo, and in silico computational approaches. Docking is one of the techniques that have seen a lot of application in microbial medication development (Nour et al. 2021).

Graphical Abstract
Strychnos innocua is a Loganiaceae plant with a straight-stem that can reach up to 18 m in height. It has multiple branches, with a trunk diameter ranging from 7 to 40 cm. Its leaves are normally simple, with a rarely rounded base. The plant is found in Sudan, Malawi, Cameroon, Uganda, and Nigeria, to name a few countries. Its root is claimed to help with gonorrhoea, while root decoction of the plant in fresh form is reported to help in the treatment of snake bites [9.10]. In Kaduna State, Nigeria, the plant can be obtained.
The root bark of this plant has been previously found to contain important chemical compositions (Ibrahim et al. 2021;Iyun et al. 2022;Sallau et al. 2022). However, there is a dearth of information regarding in silico molecular docking studies of compounds isolated from S. innocua root bark. In this research, 7-hydroxycoumarin (1) and 2,13-octadecadien-1-ol (2) were isolated from S. innocua root bark, characterized, and subjected to docking analysis. This is the first time these compounds have been isolated from this plant.

Plant collection
The plant of S. innocua was collected from the wild in Kaduna State of Nigeria. It was then identified and

Extraction
The root bark of S. innocua was dried under shade. Subsequently, it was then crushed to a fine powder. The powder (i.e., pulverized sample, 2 kg) was subjected to extraction using the maceration technique with solvents n-hexane solvent, ethyl acetate solvent, and methanol solvents, respectively, in increasing polarity as reported by Ibrahim et al. (2021); Iyun et al. 2022;Sallau et al. 2022).

General experimental procedure
GC-MS of the isolated compounds was done on GC 7890B, MSD 5977A, Agilent Tech. The NMR (1D and 2D) spectra were measured on Varian-VNMRS 400 MHz spectrometer using dimethyl sulfoxide (DMSO) for Compound (1) and chloroform (CdCl 3 ) for Compound (2) as the solvent, while ppm is the unit of the chemical shift (δ).

Reagents and chemicals used
All the reagents and chemicals used in this research (n-hexane, ethyl acetate, chloroform, and methanol) are of analytical grade.

In Silico docking studies
In silico docking studies were performed on compounds (1 and 2) and ciprofloxacin (standard drug) with target receptors (PDB: 3HO8 and 2OZ6) downloaded from www. rcsb. org. Their two-dimensional structure (2D) was generated from ChemDraw professional 16.0 and converted to three-dimensional (3D) geometrical optimization using Spartan 20v.1.1 /2020. The target receptors in three-dimensional form were prepared using Discovery Studio Visualizer and saved in PDB and then uploaded for docking studies using Pyrx. The docking output with binding score was visualized in Discovery Studio to analyze the protein-ligand interactions (Ejeh et al. 2021;Tukur et al. 2022).
The ethyl acetate extract of S. innocua (Fig. 7) revealed the presence of coumarin in the phytochemical study, and the extract showed antibacterial activity against B. subtilis, S. aureus, and P. aeruginosa . When the extract was subjected to chromatography separation, Umbelliferone and 2,3-Octadecadien-1-ol (Figs. 8 and 9) were isolated, and their structures were determined by spectroscopic analysis and compared to published data (Naka et al. 2006;Singh et al. 2010;Mazimba 2017;Hoskovec et al. 1990). Umbelliferone is found in nature in a variety of plant families and has been shown to have pharmacological effects such as antioxidants and antimicrobials (Mazimba 2017), while 2,13-octadecadien-1-ol was discovered among the major chemical constituents of Cedrela sinensis seed, and the plant's antibacterial activity in vitro was found to be significant (Lin et al. 2012).
The interactions of the compounds with the target receptors (PDB: 3HO8 and 2OZ6) were investigated using molecular docking (Tables 3 and 4) and in comparison with ciprofloxacin (standard drug). The binding scores of the compounds with S. aureus pyruvate carboxylase 3HO8 (receptor) are all moderately lower than ciprofloxacin, as shown in Table 3. Though Umbelliferone binding energy (-5.6 kcal/mol) is higher than 2,13-octadecadien-1-ol (− 4.7 kcal/mol), their interactions with the receptor are demonstrated in Figs. 10 and 11, while the binding energy of ciprofloxacin was − 6.6 kcal/mol and its interaction is presented in Fig. 12. In addition, Table 4 also demonstrates that the compounds bind to the active site of P. aeruginosa virulence factor regulator 2OZ6 (receptor) with lower binding scores than ciprofloxacin. Also, Umbelliferone has a higher binding energy (− 6.9 kcal/mol) than 2,13-octadecadien-1-ol (− 5.6 kcal/mol), their interactions with the receptor are depicted in Figs. 13 and 14, respectively. The binding energy of ciprofloxacin was − 8.7 kcal/mol, and its interactions are depicted in Fig. 15.