Structure-based multitargeted screening of bioactive compounds of Catharanthus roseus against breast cancer

Full Length Research Article 

Structure-based multitargeted screening of bioactive compounds of Catharanthus roseus against breast cancer

Abdulaziz Asiri*, Amer Al Ali, Mohammed H. Abu-Alghayth

Adv. life sci., vol. 12, no. 1, pp. 191-196, February 2025
*- Corresponding Author: Abdulaziz Asiri (Email: amfasiri@ub.edu.sa) 
Authors' Affiliations

  1. Department of Medical Laboratory Sciences, College of Applied Medical Sciences, University of Bisha, 255, Al Nakhil, Bisha – 67714 – Saudi Arabia
 

[Date Received: 13/07/2024; Date Revised: 18/11/2024; Date Published: 31/12/2024]

Abstractaa download_button
Introduction
Methods
Results
Discussion
References 

Abstract

Background: Breast cancer (BC) remains a major global challenge, with current treatments targeting hormone receptors with partial agonists/antagonists that frequently cause side effects and resistance.

Methods: This study investigates bioactive compounds of Catharanthus roseus as potential EGFR and ERα inhibitors. Protein-ligand interactions, which are important in drug design, were assessed using the PyRx 0.8 virtual screening tool. The LOTUS database was used to generate a bioactive compound library (N = 291) of C. roseus constituents. The physiochemical properties of selected hits were investigated to identify lead-like compounds.

Result: Among the screened compounds, five compounds namely, LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033 exhibited strong binding to ERα and EGFR, and interacted with key amino acid residues of ERα and EGFR proteins. These compounds have favorable physiochemical properties and meet Lipinski's criteria.

Conclusion: The compounds LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033 can be used as ERα and EGFR inhibitors for BC treatment. However, more experimental validation is needed to optimize these compounds as ERα and EGFR inhibitors.

Keywords: Breast cancer; EGFR; Erα; Virtual screening; Drug likeness 

Introduction6th button-01

Breast cancer (BC) is the most common cancer in women, and it is the second biggest cause of cancer-related death after lung cancer [1]. The World Health Organization declares an alarming increase in BC prevalence in developing countries in early 2020, citing increased life expectancy, urbanization, and adoption of Western lifestyles. BC claimed the lives of an estimated 627,000 women in 2020, accounting for around 15% of all female cancer deaths [2].

Hence, establishing effective treatment solutions for this life-threatening condition is crucial. BC chemotherapy frequently targets important receptors, including ERα (estrogen receptor alpha), progesterone receptor, and epidermal growth factor receptor (EGFR).

Estrogen, notably 17 β-estradiol, plays a crucial role in BC initiation and progression by upregulating c-Myc and cyclin D1, allowing mammary epithelial cells to migrate from G1 to S phase more efficiently. Anti-estrogen treatments are a promising and core strategy to treat ER-positive BC [3].

EGFR is especially important in triple-negative BC, where its expression is often high [4,5]. Tamoxifen, Trastuzumab, Paclitaxel, Capecitabine, Cyclophosphamide, Gemcitabine, and Docetaxel are the approved treatment drugs for BC, albeit they come with a variety of side effects [6]. Furthermore, phytochemicals and their derivatives have shown promising anti-cancer potential as an alternative therapy [7].

Computer-Aided Drug Design (CADD) is gaining popularity because of its benefits in selectivity, efficiency, efficacy, less development timelines, lesser toxicity, and better alignment with pharmacokinetic parameters [8,9]. Achieving a balance between pharmaceutical chemistry and biological activity is critical for successful medication development. With the increasing demand for new medications, selecting physiologically active structures has become more crucial.

Utilizing structural biology and computational approaches enables the development of active chemical libraries and addresses the issue of molecular obesity [10]. Catharanthus roseus is a well-known medicinal plant that has been used since ancient times. It is well-known in herbal medicine due to its anticancer bioactive compounds. C. roseus is used in Ayurveda to treat cancer, diabetes, stomach disorders, kidney, liver, and cardiovascular diseases [11].

This study aims to find C. roseus compounds as ERα and EGFR inhibitors using in-silico tools to combat BC.

Methods6th button-01

Protein preparation

The crystal structures of ERα (ID: 3ERT) and EGFR (ID: 2J6M) were retrieved from the Protein Data Bank.

The Discovery Studio Visualizer 2020 was used to remove co-crystal ligands and heteroatoms, and proteins were saved in .pdb format.

Bioactive compound library preparation

The LOTUS database acquired information about C. roseus constituents to create the bioactive compound library. 291 distinct compounds were discovered, with chemical structures, molecular weights, biological activities, and other relevant properties. The compounds were downloaded in .sdf format and then processed for energy minimization before being converted to pdbqt format with the PyRx tool.

Virtual screening

Molecular docking predicts the optimal binding mode between a ligand and a macromolecule. This technique requires a receptor and a ligand [12]. Virtual screening (VS) has emerged as a potentially successful technique for drug discovery, reducing time, cost, and resource requirements significantly [13]. The basic goal of screening is to explore chemical compound databases for new hits with the highest potential biological activity [14].

The PyRx 0.8 tool [15,16] was used to screen the prepared compound library against the ERα and EGFR active sites. Following that, a detailed interaction analysis and visual inspection were carried out to determine the most stable complex based on lower binding energy (BE) values.

Results6th button-01

This study aimed to uncover natural inhibitors for two critical targets in BC treatment: ERα and EGFR. C. roseus, a well-known medicinal plant known for synthesizing vinca alkaloids with powerful anti-cancer capabilities, was chosen for study. This plant's bioactive constituents were accessed using the LOTUS database, yielding 291 compounds.

These compounds were computationally screened against the active sites of ERα and EGFR targets. Notably, 13 compounds exhibited significant efficacy and strong BE towards both EGFR and ERα (Table 1). Among them, the top 5 compounds were selected for detailed interaction analysis.

Interaction with EGFR

Figure 1 shows a superimposed view of the top 5 compounds and the control compound (AEE-788) in the EGFR binding pocket, indicating that they bind at the same pocket.

LTS0199033 interacted with Pro794, Leu718, Ala743, Leu844, Val726, Thr854, Met766, Thr790, Glu762, Lys745, Phe723, Asp855, Met793, Gly796, and Leu792 residues of EGFR (Fig 2A). LTS0049153 was found to interact with Arg841, Asn842, Cys797, Asp800, Lys745, Thr854, Gly796, Glu762, Leu788, Thr790, Met766, Ala743, Met793, Leu792, Val726, Leu844, Asp855, and Phe723 residues of EGFR (Fig 2B). LTS0084120 interacted with Leu844, Leu792, Met793, Leu718, Pro794, His805, Glu804, Tyr801, Phe795, Gly796, Ala743, Leu788, Ile744, Thr790, Lys745, Met766, Glu762, Val726, and Gln791 residues of EGFR (Fig 2C). LTS0192836 binds with Met793, Leu718, Gly796, Asn842, Phe723, Arg841, Ala743, Asp855, Thr854, Leu844, Thr790, Gln791, Val726, and Leu792 residues of EGFR (Fig 2D). LTS0052616 was found to interact with Leu718, Pro794, Phe795, Leu792, Gly796, Met793, Val726, Ala743, Leu844, Glu762, Thr854, Met766, Thr790, Lys745, Asp855, and Phe723 residues of EGFR (Fig 2E). The control compound AEE-788 was found to interact with Gln791, Leu844, Leu792, Met793, Leu718, Pro794, His805, Glu804, Tyr801, Phe795, Gly796, Ala743, Met766, Leu788, Glu762, Thr790, Lys745, Lys745, Ile744, and Val726 (Fig 2F).

Interaction with ERα

Figure 3 shows a superimposed view of the top 5 compounds and the control compound (4-Hydroxytamoxifenin) in the ERα binding pocket, indicating that they bind at the same pocket.

LTS0049153 interacted with Ala534, Leu539, Met528, Leu536, Trp383, Leu525, Met522, Tyr526, Lys529, Lys531, Cys530, Val533, and Pro535 residues of ERα (Fig 4A); while LTS0192836 interacted with Trp383, Met522, Leu536, Leu354, Leu539, Asp351, Cys530, Val533, Lys529, Tyr526, and Glu380 residues of ERα (Fig 4B). LTS0084120 was found to bind with Tyr537, Glu380, Val533, Pro535, Leu536, Val534, Leu539, Leu354, Asp351, Trp383, Met528, Leu525, Tyr526, and Met522 residues of ERα (Fig 4C). LTS0052616 interacted with Pro535, Cys530, Val533, Met522, Lys529, Tyr526, Leu525, Leu536, Leu354, Trp383, Leu387, Ala350, Asp351, Leu539, and Val534 residues of ERα (Fig 4D). In addition, LTS0199033 was found to interact with Pro535, Cys530, Val533, Met522, Lys529, Tyr526, Leu525, Leu536, Leu354, Trp383, Leu387, Ala350, Asp351, Leu539, and Val534 residues of ERα (Fig 4E). Furthermore, Leu525, Met522, Leu387, Ala350, Asp351, Trp383, Leu354, Leu539, Leu536, Val534, Pro535, Val533, Cys530, Tyr526, and Lys529 residues of ERα was found interact with the control compound 4-Hydroxytamoxifen (Fig 4F).

Physiochemical properties

The physiochemical properties of selected hits were evaluated using the LOTUS database, which includes a variety of metrics used to identify lead-like compounds. These natural chemicals were assessed using molecular descriptors such as NP-like scores. The results reveal that all five compounds exhibit favorable properties within acceptable ranges of these parameters and adhere to Lipinski's criteria without exception (Table 2).

Figures & Tables

   

Discussion6th button-01

BC is one of the most prevalent malignancies among women globally, with around 70% of cases being ERα+. Deregulation of ERα signaling is crucial in malignancy progression. ERα is a transcription factor that promotes the production of estrogen-responsive genes, which are linked to tumor growth in BC cells [17]. EGFR is an important target for cancer treatments. Approximately 50% of triple-negative BC and inflammatory BC cases have EGFR overexpression, prompting extensive testing of EGFR inhibitors in several studies [18]. Bioactive compounds from C. roseus were screened against ERα and EGFR active sites, with 13 compounds showing strong BE towards both proteins. The top 5 compounds namely, LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033 are described in detail in this study.

The residues of ERα Leu525, Met522, Leu387, Ala350, Asp351, Trp383, Leu354, Leu539, Leu536, Val534, Pro535, Val533, Cys530, Tyr526, and Lys529 were found to interact with the control compound 4-Hydroxytamoxifen. Further, the EGFR residues Gln791, Leu844, Leu792, Met793, Leu718, Pro794, His805, Glu804, Tyr801, Phe795, Gly796, Ala743, Met766, Leu788, Glu762, Thr790, Lys745, Lys745, Ile744, and Val726 were found to interact with the control compound AEE-788. Notably, the hit compounds (LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033) interacted with the same ERα and EGFR residues, indicating that they bind to the same binding pocket as the control compounds.

In docking studies, BE is used to quantify the strength of the interaction between a ligand-protein complex, with a high negative BE indicating a stable ligand-protein complex [19-21]. Interestingly, the hit compounds (LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033) have high negative BE values for both ERα and EGFR, indicating strong interactions with both targets. In addition, H-bonding plays an important role in the stability of the ligand protein complex [22-24]. Notably, the hit compounds (LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033) form multiple H-bonds with ERα and EGFR residues.

Natural resources, including phytochemical-rich herbal plants, are thought to be safer and more effective than synthetic agents for treating chronic and infectious diseases due to their fewer side effects [25]. C. roseus, a medicinal plant from the Apocynaceae family, has a long history of use in Ayurvedic and traditional Chinese medicine. Research has demonstrated its potential in cancer treatment [26]. This study found that bioactive compounds from C. roseus bind strongly to ERα and EGFR proteins, suggesting their potential as anticancer agents.

EGFR and ERα play key roles in the progression of BC. EGFR increases cell proliferation and survival via a variety of signaling pathways and is frequently associated with aggressive malignancies. Endocrine therapies aim to target ERα, a nuclear hormone receptor that promotes hormone-dependent BC growth. Bioactive compounds from C. roseus were screened to target EGFR and ERα. Five compounds (LTS0049153, LTS0192836, LTS0084120, LTS0052616, and LTS0199033) demonstrated strong binding to ERα and EGFR, interacting with key amino acid residues of both targets ERα and EGFR. These compounds have favorable physiochemical properties and meet Lipinski's criteria, suggesting potential as ERα and EGFR inhibitors for BC treatment. Further experimental validation is required to optimize these compounds as ERα and EGFR inhibitors.

Acknowledgement

The authors extend their appreciation to the Deanship of Graduate Studies and Scientific Research at University of Bisha for funding this research through the general research project under grant number (UB-GRP- 39 -1444).

Author Contributions

The authors are thankful to the Deanship of Graduate Studies and Scientific Research at the University of Bisha for supporting this work through the Fast-Track Research Support Program.

Conflict of Interest

The authors declare that there is no conflict of interest regarding the publication of this paper.

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