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Patala, R., Anggi, V. Pharmacophore Modeling and Molecular Docking of Flavonoid Derivatives in Abelmoschus manihot Against Human Estrogen Receptor Alpha of Breast Cancer. Sciences of Pharmacy 2022, 1(2), 1-9.

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Patala, R, Anggi, V. Pharmacophore Modeling and Molecular Docking of Flavonoid Derivatives in Abelmoschus manihot Against Human Estrogen Receptor Alpha of Breast Cancer. Sciences of Pharmacy. 2022; 1(2):1-9.

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Recky Patala, Viani Anggi. 2022. "Pharmacophore Modeling and Molecular Docking of Flavonoid Derivatives in Abelmoschus manihot Against Human Estrogen Receptor Alpha of Breast Cancer" Sciences of Pharmacy 1, no. 2:1-9.

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Pharmacophore Modeling and Molecular Docking of Flavonoid Derivatives in Abelmoschus manihot Against Human Estrogen Receptor Alpha of Breast Cancer

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Home / Sciences of Pharmacy / Volume 1 Issue 2 / 10.58920/sciphar01020001

Research Article

Pharmacophore Modeling and Molecular Docking of Flavonoid Derivatives in Abelmoschus manihot Against Human Estrogen Receptor Alpha of Breast Cancer

by Recky Patala , Viani Anggi

Academic editor: Keerthic Aswin
Sciences of Pharmacy 1(2): 1-9 (2022);
This article is licensed under the Creative Commons Attribution (CC BY) 4.0 International License.

30 Aug 2022
21 Sep 2022
26 Sep 2022
03 Oct 2022

Abstract: Tamoxifen is the most commonly used anti-estrogen adjuvant therapy for estrogen receptor-positive breast cancer. However, it is associated with an increased risk of some serious side effects, such as uterine cancer, stroke, and pulmonary embolism. The flavonoid compounds in the leaves of A. manihot inhibited the growth of 4T1 breast cancer cells at a CTC50 concentration of 185.06 μg/ml. Therefore, this study aims to examine the molecular interactions and pharmacophore modeling based on the interaction of 4-OHT with human ER, followed by the molecular docking of the flavonoid derivatives with human ERα. The molecular docking simulations and 3D structure-based pharmacophore models were used to identify the molecular interactions of flavonoid derivatives in A. manihot on estrogen receptors (ERα) (PDB ID: 3ERT). The results showed that the binding energies of the flavonoid derivatives in isorhamnetin and isoquercitrin were -8.68 kcal/mol and -8.75 kcal/mol, respectively. This compound also interacted with Arg394 and Glu353 important amino acid residues in the ERα-binding pocket. Meanwhile, the pharmacophore fit scores of isorhamnetin and isoquercitrin were 82.36% and 84.91%, respectively. The flavonoid derivatives in A. manihot had pharmacophore fit resulting from the 4-OHT complex with ER, and therefore they had potential as ERα antagonists. Out of the 10 flavonoid derivatives, isorhamnetin and isoquercitrin showed the best docking scores and could be used as candidates for new anti-breast cancer drugs with antagonistic activity against ERα.

Keywords: Abelmoschus manihotEstrogen Receptor AlphaMolecular DockingPharmacophore

1.          Introduction

Cancer is currently the leading cause of death worldwide. In 2020, almost 10 million deaths were registered as a result of cancer, and according to report, breast cancer ranks first with 2.26 million cases and 685,000 deaths (1). Estrogen receptors are the human prognostic marker used to identify tumors in breast tissue (2), and they consist of two subtypes, ERα and ERβ, which have different affinities for estrogen. ERα is a transcription regulator-activated ligand as a major regulator of breast differentiation and proliferation (3). Furthermore, it plays an important role in the development and progression of hormone-dependent breast cancer (4). Tamoxifen, as an antiestrogen can block estrogen signaling through a mechanism of competition with endogenous estrogens to bind to the estrogen receptor and alter its activity as a regulator of gene transcription. Additionally, it has antagonistic activity in the breast but is an agonist in the uterus and bone (5). Tamoxifen and its active metabolite 4-hydroxytamoxifen (4-OHT) have cytotoxic activity against MCF-7 breast cancer cells with an IC50 of 5 μM and 1 μM (6). However, the effectiveness of tamoxifen is limited by the presence of intrinsic resistance. Amplification and overexpression of COPS5 (complex subunit COP9) was a major cause of tamoxifen resistance in 86.7% of patients with ERα-positive breast cancer. Overexpression of COPS5 through isopeptidase activity leads to proteasome-mediated NCoR degradation, which is a major repressor of ERCC, and therefore, alternative medicine is needed (7).

Flavonoids are one of the promising natural remedies for breast cancer (8). One of the plants that contain active flavonoid compounds is Abelmoschus manihot L. Medik. Most people in Palu and Manado cities, Indonesia use the leaves as food, which were reported to have total flavonoids of 61.763% (9). It was reported that the flavonoid compounds in the leaves of A. manihot inhibited the growth of 4T1 breast cancer cells at a concentration of 50% inhibitory cell growth (CTC50) of 185.06 μg/ml (10). Furthermore, flavanoid compounds can act as selective estrogen receptor modulators (SERMs) as they are a group of compounds with a C6-C3-C6 chemical structure. SERMs can enter the cell and then bind to the ER, forming a complex bond. This complex binding binds to the Estrogen Response Element (ERE), which is located near the gene whose transcription is controlled. Additionally, the complex will activate nuclear receptor co-repressor (NCoR) protein and suppress cancer cell replication, therefore its proliferation can be controlled (11,12). Currently, studies on pharmacophore and molecular docking of flavonoid derivatives in A. manihot to ERα are very limited. Therefore, it is necessary to conduct pharmacophore modeling tests based on the interaction of 4-OHT with human ERα followed by molecular docking of flavonoid derivatives of A. manihot with human ERα.

2.          Experimental Section

2.1       Hardware and Software

The hardware used is a computer with Windows 10 64-bit OS, AMD A6-7310 APU Processor with AMD Radeon R4 Graphic 2.00 GHz and 6 GB RAM. The software is ChemDraw professional 15.0 (Academic License), LigandScout 4.4.5 Advanced (Universitas Padjadjaran License), AutoDock 4.2.6, AutoDockTools 1.5.6 (The Scripps Research Institute), and BIOVIA Discovery Studio 2021 (Academic License).

2.2       Preparation of Ligands and Molecular Docking

3D X-ray crystallographic structure of ERα in complex with 4-OHT (PDB ID: 3ERT) crystallized and stored by Shiau et al., (1998) 1.90 Å resolution downloaded from the Protein Data Bank online ( /structure/3ERT) (13). The ligands were separated from the receptor structure using the BIOVIA Discovery Studio 2021 R2 client. The 3D-mangostin structure and its derivatives as ligands were optimized by ChemOffice 2010 and ChemDraw Ultra 12.0 (PerkinElmer Inc.) and LigandScout 4.4.5 Advanced (Inte: Ligand GmbH). Molecular docking simulations were carried out according to previous validation studies (14). ERα receptors and ligands were prepared for docking simulation using AutoDockTools 1.5.6. Furthermore, receptors as macromolecules are added with Kollman charges, while ligands are added with Gasteiger charges (15). The grid parameter file corresponds to a grid consisting of 40×40×40 points spaced 0.375Å and centered on the active edge ERα (x = 30,010, y = -1,913, and z = 24,207). AutoDock 4.2.6 (The Scripps Research Institute) was used to perform molecular docking simulations. The docking parameter file corresponds to the Lamarckian Genetic Algorithm (LGA) with 100 run counts, 150 population sizes, 2,500,000 energy evaluations, 0.02 gene mutation rate, and 0.8 crossover rate (16). The conformational results from the simulation were grouped using the root mean square deviation (RMSD) tolerance of 1.0. The ligand conformation with the lowest free bond energy (∆G) was selected from the best cluster, and the best ligand conformation was used for the next analysis stage. The receptor-ligand complex from the docking simulation was visualized using the BIOVIA Discovery Studio Visualizer 2021. The determination of ligand interaction features for each pose in the receptor-binding pocket was analyzed with LigandScout 4.4.5 Advanced Inte: Ligand GmbH. Wina, Austria (8).

2.3       3D Structure-based Pharmacophore Modeling

Structure-based 3D pharmacophore modeling was derived from an ERα X-ray structure complexed with 4-OHT (PDB ID: 3ERT) using Ligandscout 4.4.5 Advanced (17). Feature validation was performed by filtering 626 active sets and 20,773 bait sets obtained from the Database of Useful Decoys (18). The flavonoid derivatives in A. manihot were screened virtually using a 3D structure-based pharmacophore model validated with the LigandScout 4.4.5 advanced algorithm. The result of this process is the adjustment value of the pharmacophore. The pharmacophore-fit score was used to measure the feature and geometry similarity of each achieved compound based on a 3D structure with a feature pharmacophore model with 4 feature counts removed for the combined pharmacophore, 10.0% optional threshold partial adaptation feature, and 1.0 feature tolerance scale factor.

3.          Result and Discussion

Two hydrogen bonds were observed in the interaction between 4-OHT and human ERα. Hydrogen bonding was observed in the interaction between 4-OHT and human ERα bound to Glu353 as a hydrogen bond donor (HBD) and Arg394 as a hydrogen bond acceptor (HBA), as shown in Figure 1.

Figure 1. Interaction of hydrogen bonds between 3D (left) and 2D (right) structure 4-OHT with Arg394 and Glu353 in human ERα (Black dotted lines indicate hydrogen bonds, salt bridges, and metal interactions. Solid green lines indicate hydrophobic interactions).

The hydrophobicity of 4-OHT mostly interacts with the aromatic ring and the butenyl group also forms positive ionized interactions with the secondary amine nitrogen. Hydrogen bond interactions are formed with hydroxyl oxygen and phenoxy as shown in Figure 2.


Figure 2. (left) 3D structure-based pharmacophore modeling of 4-OHT with ERα (PDB ID: 3ERT) (The interactions of positively ionizable hydrophobic hydrogen bond donors and acceptors are represented as blue stars, yellow balls, green and red arrows). (right) 2D structure-based 3ERT shows the hydrophobic interactions with the binding pocket residues.

ERα has a ligand-binding domain (LBD) that is primarily a hydrophobic cavity composed of amino acid residues of helices 3, 6, 7, 8, 11, and 12. The agonist and antagonist activities of the ligands are determined by helix-12 of residue 536- 544 in its macromolecule (ERα). When a 4-OHT antagonist of ERα binds to LBD, helix-12 will be closed and not bound to the co-activator, and therefore it has antagonistic activity based on the absence of hydrogen bonding interactions with His524 (14). Based on the interaction between 4-OHT and the pharmacophore features of human ERα, two features of four aromatic rings of HBD and one HBA were produced using LigandScout.

Molecular validation of the docking was performed by rebinding the co-crystallized 4-OHT to its original position at the human ERα binding site. The results show a binding mode similar to that of the original complex. The 4-OHT molecule interacts with Arg394 and Glu353. The validity of the docking program was confirmed by placing the 4-OHT pose, which was re-docking with the original resulting in an RMSD value of 0.590. This value is defined as valid as shown in figure 3.

Figure 3. Superimposition of the original and re-docking 4-OHT molecule (RMSD = 0.590).

The best docking conformation of isorhamnetin and isokesitrin in the ERa ligand-binding domain is indicated by the presence of hydrogen bonds with Arg394 and Glu353 important amino acid residues in the human ERα binding pocket and with other amino acid residues as shown in Figure 4.