CHAPTER 1

Introduction

Anchor 1

Background of the Study

Medicinal plants have a rich history of use in combating diseases, dating back to ancient times (Pretrovska, 2012). Throughout the ages, various parts of plants, including leaves, stems, roots, and more, have been harnessed for their therapeutic properties in the treatment of human ailments (Mintah et al., 2019). However, as the field of medicine progresses hand in hand with technological advancements, it becomes imperative to develop efficient and scientifically backed approaches to cure the growing number of identified diseases. Technology is playing a crucial role in this advancement, and one notable contribution to the medical field is the use of phytochemical-protein screening, which aims to identify the specific phytochemicals in medicinal plants that interact with various protein targets to restore the overall equilibrium of cells (Ding et al., 2009).

In the realm of medicinal plants, Vitex negundo, commonly known as Lagundi, has been found to possess noteworthy properties in the treatment of skin diseases such as eczema and ringworm (Medical Health Guide, n.d.). Tandon and Gupta (2006) conducted a study titled "Vitex negundo Linn leaf extract as an adjuvant therapy to standard anti-inflammatory drugs," which sheds light on the benefits of Lagundi extract as an adjunct to conventional anti-inflammatory drugs. Moreover, Zheng et al. (2015) revealed that Vitex negundo exhibits versatile pharmacological activities due to its complex bioactive composition. Taking into consideration the bioactive makeup of Lagundi and the recommendation by Nadkarni (1976) regarding its use in treating psoriasis, researchers have embarked on a study to investigate the medicinal potential of Lagundi as a plant-based remedy for psoriasis.

Psoriasis is a chronic immune-mediated inflammatory skin condition primarily affecting areas such as the elbows, knees, scalp, and lower back, but it can manifest on any surface of the skin (Griffiths & Barker, 2007). This dermatological disorder is characterized by the presence of inflammatory cells in the epidermis, lesions, and silver-white scales. While psoriasis is considered a chronic condition, various treatment options exist to effectively manage its symptoms (NHS UK, 2022). In the quest for more cost-effective alternatives in psoriasis treatment, herbal medicines have emerged as a prominent component of complementary and alternative medicine (Better Health, 2021). To explore the potential of herbal medicines, the researchers in this study will employ in silico methods, which offer the advantage of accelerating the rate of discovery while reducing the need for expensive laboratory work and extensive clinical trials, if implemented correctly (Brogi et al., n.d.).

In silico studies involve the use of computational models to simulate and analyze phytochemical-protein interactions (Fielden et al., 2002). One popular methodology in these studies is reverse screening, which aims to identify proteins that can be targeted by specific compounds, such as phytochemicals (Huang et al., 2018). This approach generates novel predictions by utilizing experimentally validated Phytochemical-Protein Interactions (PCPI) (Briones et al., 2021). Additionally, Liu et al. (2016) have developed a network visualization tool that enables the prediction of relationships among phytochemicals, protein targets, enriched pathways, and diseases, facilitating a comprehensive understanding of their interconnections.

While several in silico methods are currently employed to determine the multi-targeted action of herbal plants (Yi et al., 2018), there is a notable lack of representation regarding the use of Lagundi in psoriasis treatment through in silico analysis. Therefore, the researchers aim to bridge this gap in the natural products sector by implementing a scientifically validated in silico method.

Statement of the Problem

This study focuses on exploring the interaction between phytochemicals from Vitex negundo and proteins related to psoriasis. It aims to create a network visualization to demonstrate the connections and interactions between these phytochemicals and the disease proteins involved in the psoriasis pathway. The study utilizes in silico methods and adapts a novel workflow from previous research. To validate the experiment, known phytochemicals that target psoriasis-related proteins within the disease pathway will be used as a control group. The study seeks to answer specific research questions related to this interaction.

What are the bioactive components that target the proteins within the disease pathway?
What are the statistically overrepresented target disease proteins by the phytochemical based on g:profiler?
Is there a significant difference in the phytochemicals between the established control group and the experimental group in terms of:

a. Docking scores

b. Bioavailability

c. Gastrointestinal absorption

d. Lipophilicity

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Scope & Limitations

This study focuses on the evaluation of the phytochemical-protein interaction of Vitex negundo against psoriasis. It will be conducted in silico using a novel workflow adapted from a previous study titled “Visualizing Phytochemical-Protein Interaction Networks: Momordica charantia and Colorectal Cancer” by Briones et al. (2021), where it used a computational device rather than a laboratory. The data to be used will be gathered from prior studies from various databases that have been validated and scientifically experimented with.

Moreover, this research will not include any medicinal plants other than Vitex negundo. Other diseases other than psoriasis are also not covered by this study. With their strategy, the researchers will be able to identify the characteristics of Vitex negundo and how it can affect psoriasis.

Significance of the Study

This research aims to provide scientific findings and knowledge regarding the interaction of phytochemicals of Lagundi and disease proteins within the pathway of psoriasis. The findings of this study could be beneficial to the following.

This sector will benefit greatly from the results of this study. Not only can network visualization help with the future of creating medicine, but it can also help alleviate the time and effort it usually takes for the study alone. The natural products sector, being solely focused on products harvested in the wild, grown as cultivated crops, or grown in agroforestry systems, is employed in various businesses for pharmaceutical, nutraceutical, cosmetic, and other industrial and health purposes.

Natural Product

Sector

The medical sector can also take advantage of this study regarding the details of the disease the researchers are tackling. They can also focus more on the pharmacological properties from the results of this study for the betterment of the medical sector, such as in natural product medicines and treatments for the said illness.

Medical

Sector

With the interest of the medical sector, the agricultural sector can also gain from this study considering Lagundi is common in Southeast Asia, specifically the Philippines. The agricultural sector could implement an impactful program that would specialize in the modernization of agriculture for a more beneficial association with the medical field.

Sector

Agricultural

The study would also be beneficial to future researchers with topics concerning the variables discussed in this study. With this study, they can also determine the scope and limitations of the study that they will be conducting.

Future

Researchers

Definition of Terms

The extent to which ingested bioactive compounds reach and be absorbed by the circulatory system and be used by the body by acting on specific sites (Shi et al., 2022). A property that will be measured in both the control group and the experimental group.

BIOAVAILABILITY

It refers to the calculated noncovalent three-dimensional interactions between a ligand and a protein or a targeted binding site. (Berenger et al., 2021). Another property that will be measured in both the control group and the experimental group.

DOCKING SCORES

A public web server used to analyze gene lists generated from genomic data mining. It helps identify common knowledge like pathways, biological processes, molecular functions, subcellular localizations, and shared TF-binding sites (TFBS) for input genes. In our psoriasis study, G:profiler will be crucial in determining disease-related proteins within pathways.

G:PROFILER

GASTROINTESTINAL ABSORPTION

It refers to computational models that investigate pharmacological hypotheses using methods like databases, data analysis tools, data mining, homology models, machine learning, pharmacophores, quantitative structure-activity relationships, and network analysis tools (Moore, 2021). In this study, it is the method that will be utilized to provide crucial information or speed up the discovery before conducting in vivo and in vitro studies.

IN SILICO STUDY

It implies the use of cells, tissues, or other biological components that have been isolated from the target living organisms (Dornell, 2020).

IN VITRO STUDY

It involves testing on or using complete animals, plants, or living cells (Dornell, 2020).

IN VIVO STUDY

NETWORK VISUALIZATION

It involves the visualization of relationships between data elements (John Hopkins, n.d.). In this study, the data that have gone through the specific steps mentioned in the methods will be visualized and will be presented with network visualization.

PHYTOCHEMICAL-PROTEIN INTERACTION NETWORKS

This encodes the information in several dimensions, such as PPIs, subcellular localization, phytochemical class, and pharmacokinetic parameters (Briones et al., 2021). In this study, PCPI will be the source of the data regarding the properties of Vitex negundo and psoriasis from prior studies.

PHYTOCHEMICAL

These are bioactive nutritional plant compounds found in fruits, vegetables, grains, and other plant foods that can minimize the risk of serious chronic diseases (Jimenez-Garcia, 2018). In this study, the phytochemicals are focused on the bioactive components of the Vitex negundo or Lagundi that target the proteins within the disease pathway.

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