Network pharmacology of lycopene and Molecular Docking with Top Hub Proteins

Background Lycopene is one of the potent antioxidants in the family of carotenoids that scavenges Reactive Oxygen Species (ROS) singlet oxygen which has been associated with various pathological consequences including atherosclerosis myocardial infarction, and stroke and Sex hormone-induced cancers like breast cancer, endometrial cancer and prostate cancer. As multiple pathways are involved in the manifestation of aforementioned diseases initiated at the behest of ROS, it would be appropriate to understand the likely pathways triggered by the ROS and its eventual control by the action of lycopene through network pharmacology study, a robust paradigm for drug discovery via modulation of multiple targets. Results 124 proteins were mined from CTD and STITCH databases, which showed some relationship with lycopene, among them strong association was found with TP53, STAT3 and CDK1 proteins. Lycopene showed a strong affinity with these proteins by hydrophobic interactions. Conclusion The topological analysis of a network created by the lycopene relevant genes showed its role as a potential therapeutic agent in cancer which further requires in vitro and in vivo studies to confirm these findings.


1.Background
Lycopene belongs to the carotenoids family, a class of compounds present in certain fruits and vegetables (1) which is of nutritional interest as its metabolism mediates various signaling effects (2). Lycopene undergoes extensive isomerization, a trans configuration of lycopene is found in fruits and vegetables (3,4) that gives the red hue whereas, it isomerizes in blood plasma and tissues after absorption into cis isomers (2,4). Lycopene is the most abundantly found carotenoid in the human body which is one of the most potent antioxidants that scavenges reactive oxygen species (ROS) singlet oxygen (5). Lycopene is a tetraterpene merged from eight isoprene units that are composed of carbon and hydrogen and it's an open-polyene chain, without the ionone ring as in β-carotene, gives this molecule with an advantage of a very high antioxidant capacity, which is significantly higher than any other carotenoids, namely, more than twice that of β-carotene and about 10 times higher than that of α-tocopherol (6,7). Particularly, it is effective in the quenching of superoxide anion free radicals, (6).
Therefore, its main protective mechanism is in its antioxidant properties, which have been well characterized in vitro (8).
Various mechanisms have been postulated by which lycopene alleviates diseases such as prevention of oxidative DNA damage (15) and balancing

Data curation
Lycopene was found to be associated with 124 curated genes/proteins, Table 1, from the STRING database with a medium confidence level of 0.4 and was reviewed on the UniProt database to create a network.

Network construction and analysis
Based on the STRING database evidence, the network was constructed with lycopene associated proteins to build the protein-protein interaction

Gene Ontology analysis
To explore the functional characteristics of lycopene associated genes were subjected to GO analysis and enriched according to the available GO annotations with gene ID and gene accessions in the PANTHER database.
In Fig 3 a, molecular function the genes associated with lycopene showed the highest activity in the catalytic activity. In Fig 3 b, the biological process, the associated genes had maximum involvement in the cellular process. In Fig 3 c,

Molecular docking analysis of lycopene
Top proteins from network analysis were used for docking. Molecular docking analysis of lycopene was performed using Auto Dock Vina Tool and their binding energy was noted. AutoDock Vina results were analyzed based on the interactions between hub proteins and ligand molecule, Table 3. The accuracies of the results were confirmed by considering the lowest binding free energy and hydrophobic binding between the receptor and ligand. The binding energy lycopene with proteins TP53 was − 6.3 kcal/ mol, STAT3 was -6.4kcal/mol and CDK1 was − 5.9 kcal/mol , Table   3.
No, any hydrogen bonds were found in all docking interactions. The hydrophobic interaction profile is shown in Fig 4, Based on the results, it can be inferred that all three proteins can bind with lycopene, which can be further validated by in vitro and in vivo studies.

3.Discussion
Network pharmacology is a relevantly new emerging technique for drug discovery approach, it's an effort to address the side effects and toxicity of drug (Hopkins 2007 In the simple parameters, obtained after network analysis, the clustering coefficient was found to be 0.795, which signifies at a higher degree, nodes tend to cluster together. The largest distance between the two nodes is 12 which is the diameter of the network whereas the shortest distance between any two nodes is 1 which is the radius of the network.
Network centralization is 0.063 which means that the network is more uniformly connected. The nodes have an average shortest path length of 4.639 and at an average number single node has 9.461 neighbors.
Network heterogeneity is the tendency of the network to contain the hub nodes which is 0.717.
In the molecular function, the proteins associated with lycopene showed the highest activity in the catalytic activity followed by binding and transporter activity whereas in the biological process the associated

4.Conclusions
The topological analysis of a network created by the lycopene relevant genes showed its role as a therapeutic agent in cancer. Furthermore, the docking results also supported a good affinity binding with TP53, STAT3, and CDK1. Since the bioavailability of lycopene is less and it is converted to a metabolite that may show different affinity with these proteins.
Hence, encapsulated lycopene can be used to confirm these in silico findings in vitro and in vivo studies.

5.Methods
All the programs were run on a 4.00 GB RAM Intel® Core i3 2.5GHz with a 64-bit Windows 10 Operating System in the HP notebook. The research approach was executed by implementing the following methods:

Data acquisition
For the identification of target genes/proteins associated with lycopene relevant to Homo sapiens, data mining was carried from CTD (34)

Gene Ontology analysis
To know the functional association of obtained genes from databases with lycopene, GO enrichment analysis using PANTHER (42) was performed. It

Network construction
The

Molecular docking study of the top hub node
The top three hub proteins, namely, TP53, STAT3, and CDK1, identified through network analysis were subjected to molecular docking study.