|Year : 2022 | Volume
| Issue : 1 | Page : 44-49
Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer
Agnia Purnama1, Diva Rayyan Rizki2, Intan Qanita2, Muhammad Iqhrammullah3, Khairunnas Ahmad1, Vivi Mardina4, Kana Puspita5, Kartini Hasballah6
1 Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Syiah Kuala, Banda Aceh, Indonesia
2 School of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
3 Department of Chemistry, Faculty of Mathematics and Natural Science, Universitas Syiah Kuala; Graduate School of Mathematics and Applied Sciences, Universitas Syiah Kuala, Banda Aceh, Indonesia
4 Department of Biology, Faculty of Engineering, Universitas Samudra. Jl. Prof. Dr. Syarief Thayeb, Meurandeh, Langsa Lama, Langsa, Aceh, Indonesia
5 Department of Chemistry Education, Faculty of Education and Teacher Training, Universitas Syiah Kuala, Banda Aceh, Indonesia
6 Department of Pharmacology, Faculty of Medicine, Universitas Syiah Kuala, Banda Aceh, Indonesia
|Date of Submission||20-May-2021|
|Date of Decision||01-Aug-2021|
|Date of Acceptance||17-Dec-2021|
|Date of Web Publication||21-Jan-2022|
Dr. Kana Puspita
Department of Chemistry Education, Faculty of Education and Teacher Training, Universitas Syiah Kuala, Darussalam, Banda Aceh
Source of Support: None, Conflict of Interest: None
A natural bioactive compound named calotropone has been reported as a drug candidate for several cancers, including pancreatic cancers. Herein, we used molecular docking approach to test the possible mechanisms of action of calotropone in inhibiting the growth of pancreatic cell cancer with gemcitabine as the positive control. By employing AutoDock Vina, we studied the molecular interaction between calotropone and pancreatic cancer-associated proteins, namely Glucosaminyl (N-Acetyl) Transferase 3, Glutamic-Oxaloacetic Transaminase 1, Tyrosine-protein kinase Met (c-Met), peroxisome proliferator-activated receptor γ, Budding Uninhibited by Benzimidazole 1, A Disintegrin and Metalloproteinase 10, Sex-determining region Y and Nuclear Factor kappa Beta (Nf-Kβ). Higher affinity energies of calotropone toward the aforementioned proteins (ranging from ‒7.3 to ‒9.3 kcal/mol) indicate that calotropone may work in the same manner as anticancer drug gemcitabine. Highest docking score was found at the interaction of calotropone and Nf-Kβ (‒9.3 kcal/mol).
Keywords: Calotropis gigantea, calotropone, molecular docking, nuclear factor kappa beta, pancreatic cancer
|How to cite this article:|
Purnama A, Rizki DR, Qanita I, Iqhrammullah M, Ahmad K, Mardina V, Puspita K, Hasballah K. Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer. J Adv Pharm Technol Res 2022;13:44-9
|How to cite this URL:|
Purnama A, Rizki DR, Qanita I, Iqhrammullah M, Ahmad K, Mardina V, Puspita K, Hasballah K. Molecular docking investigation of calotropone as a potential natural therapeutic agent against pancreatic cancer. J Adv Pharm Technol Res [serial online] 2022 [cited 2023 Mar 31];13:44-9. Available from: https://www.japtr.org/text.asp?2022/13/1/44/336200
| Introduction|| |
According to recent global epidemiological study on pancreatic cancer cases, numbers of incidence and mortality will keep increasing. In 2020, the global mortality rate for pancreatic cancer reached 90%, where difficult early diagnosis is the main cause. Nevertheless, administration of chemotherapy has been reported to give significant success on the treatment.
Gemcitabine has been assigned as a standardized chemotherapeutic drug against pancreatic metastases. However, natural compounds have also become the focus of anticancer drug development due to their significant effective medicinal properties. Several plant-derived compounds are potential for pancreatic cancer treatment., Recently, Calotropis gigantea has been in the research spotlight due to its contents of multiple antiproliferative secondary metabolites. A study in vivo using pancreatic cancer cells (panc-1) revealed the superior anticancer properties of calotropone (one of secondary metabolites from C. gigantea), in comparison with gemcitabine. In the same research, the IC50 of calotropone was observed to be as low as 18.7 μM.
Despite its high potential in treating pancreatic cancer, the mechanism of action of calotropone in inhibiting the cell growth and inducing apoptosis is still scarcely reported. In silico studies by means of molecular docking may aid the research in mapping the potential mechanism. Molecular docking has been implemented as a method of analyzing new drugs against their target proteins by predicting the affinity and activity of the compound. This method relies on the three-dimensional (3D) structure information of a protein target and the electronics of the ligand to the protein target.
Several pancreatic cancer-related proteins are the primary target of researchers in developing drugs. Glucosaminyl (N-Acetyl) Transferase 3 (GCNT3), Mucin Type GCNT3, Glutamate oxaloacetate transaminase 1 (GOT1), Tyrosine-protein kinase Met (c-Met), peroxisome proliferator-activated receptor (PPAR) γ, and Budding Uninhibited by Benzimidazole 1 (BUB1) are proteins that play a role in tumor cell development through the multiple schemes.,,, A Disintegrin and Metalloproteinase 10 (ADAM10) and Sex-determining region Y (SOX2) play a role in immune regulation in pancreatic cancer cells., Nuclear factor kappa beta (Nf-Kβ) is an inhibitory protein in apoptosis. These aforementioned proteins have been proven to be regulated by gemcitabine. Therefore, by employing the molecular docking on those proteins and comparing the results with that of gemcitabine, we can obtain the information of possible main mechanism of calotropone. Study of calotropone interaction with the therapeutic molecular target of pancreatic cancer by means of molecular docking is the novelty of this work.
| Methods|| |
Hardware and software
Docking simulation was performed on Intel Celeron N3350 Acer computer, 1.00 GB memory processor (RAM), 32-bit operating system, Windows 10 pro. Softwares used in this experiment were LigPlot + 1.5.4, PyMOL 2.4 (Delano Scientific LLC, Italy), and AutoDock Vina supported by AutoDock Tools 5.6.
The docking study analyzed calotropone compounds which cytotoxic compounds obtained based on literature. Target proteins used in this present studies are similar to our previous research, where the preparation details had been presented. The 2D structure of calotropone (CID: 70680255) and gemcitabine (CID: 60750) (for comparison) was obtained from the website (www.pubchem.ncbi.nlm.nih.gov). The ligand structure was converted from SDF format. into PDB format using Pymol 2.4 software. Ligand structures were also prepared using AutoDockTools 1.5.6.rc3 software La Jolla, California, USA. The preparation of proteins and ligands was docking with size validation and grid box separation. The parameter observed from this simulation represents the energy of the ligand affinity for the protein target. Hydrogen interactions, hydrophobic interactions, and bond distances were visualized using LigPLot + 1.5.4 (2D) and PyMOL 3.1 (3D).
| Results and Discussion|| |
Calotropone is a derivative of a natural steroid compound known to be an agent for cancer treatment., This inhibitory activity led us to study the systematic mechanism of calotropone compounds against proteins of pancreatic cancer cells. The results of the molecular docking of gemcitabine and calotropone toward the focused proteins have been presented [Table 1].
|Table 1: Comparative affinity energy and molecular interactions of calotropone dan gemcitabine with proteins|
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From the docking results, each affinity value exceeds ‒5 kcal/mol confirming the role of the ligand in regulating the protein. The most efficient bonding is shown by calotropone with Nf-Kβ owing to its energy affinity approaching ‒10 kcal/mol. Nf-Kβ is a transcription protein factor that plays a role in tumorigenesis in several types of tumors. In pancreatic cancer cells, this protein has a role in the activation of oncogenic mutations of Kras (pancreatic cancer promoters). Gemcitabine, which is the standard drug for pancreatic cancer patients, has a smaller affinity value of ‒6.3 kcal/mol. Calotropone equally has a stable affinity for the GCNT3 (‒9.0 kcal/mol). GCNT3 is a protein-coding gene that plays a role in mucin biosynthesis. Upregulation of mucin biosynthesis has an active role against Kras mutations and increases cell proliferation. Calotropone interactions with other proteins, GOT1, c-Met, PPARG, BUB1, SOX2, and ADAM10 possess good binding affinity with values ranging from ‒7.3 to ‒8.9 kcal/mol, where these values are higher than that of gemcitabine. The displays of ligand-protein interactions and their overlay in the active pocket for calotropone [Figure 1] and gemcitabine [Figure 2] have been presented.
|Figure 1: Interaction of calotropone with pancreas cancer proteins. (a) Glucosaminyl (N-Acetyl) Transferase 3. (b) Glutamic-Oxaloacetic Transaminase 1. (c) c-Met. (d) Peroxisome proliferator-activated receptor G. (e) Budding uninhibited by benzimidazole 1. (f) Nuclear factor kappa beta. (g) Sex-determining region Y. (h) A Disintegrin and Metalloproteinase 10; (i) Pose view of interaction of calotropone with proteins. (ii) Overlay of calotropone in active pockets of proteins|
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The ligand and protein affinity occurs because of the hydrophobic and polar hydrogen interactions. In the case of Nf-Kβ, calotropone has polar hydrogen with amino acid Phe151 (3.5 Å) at N terminal and Å Met208 (2.7 Å) at C terminal [Figure 1]. Compared with drug ligand, amino acids that interacted with gemcitabine are different. They are His67 (3.16 Å), dc15 (3.26 Å), dc13 (3.30 Å), dc13 (3.09 Å), dc14 (3.14 Å) and Arg-59 (3.12 Å) [Figure 2]. The interaction of Met208 and calotropone established the strongest bond with a bond length of 2.7 Å affecting the affinity energy. Previous analysis showed Met208 as one of the amino acids that play a role in the growth of B-cell activating factor (BAFF). The binding of inhibitor with Met208 causes the decrease of Nf-Kβ p65 activation via BAFF effect. Hydrophobic interaction of calotropone also inhibits Nf-Kβ through Lys147, Thr205, Lys148, Val150, Glu152, and Lys206 amino acids while gemcitabine maintains fewer bonds, namely Arg57 g [Table 1]. The affinity value of calotropone in GCNT3 and c-Met is higher than that of gemcitabine because calotropone has more polar hydrogen and hydrophobic interactions due to the hydrogen interactions, except for GOT 1. BUB1 PPARG, SOX2, and ADAM10 which bind to calotropone are only superior in hydrophobic interactions. From the results of the dockings, calotropone binds to 7 amino acids in BUB1, 10 amino acids in PPARG, 10 amino acids in SOX2, and 9 amino acids in ADAM 10, while gemcitabine binds 4 amino acids in BUB1, 8 amino acids in PPARG, 3 amino acids in SOX2, and 8 amino acids in ADAM 10. SOX2 is a regulatory protein on ADAM10 and has a function in pancreatic cancer cell immunity. The suppression of SOX2 can suppress ADAM10 expression. This shows the inhibition of ADAM 10 by calotropone can be carried out via SOX2 or directly targeting the protein (ADAM10).
|Figure 2: Interaction of gemcitabine with pancreas cancer proteins. (a) Glucosaminyl (N-Acetyl) Transferase 3. (b) Glutamic-Oxaloacetic Transaminase 1. (c) c-Met. (d) Peroxisome proliferator-activated receptor G. (e) Budding Uninhibited by Benzimidazole 1. (f) Nuclear factor kappa beta. (g) Sex-determining region Y. (h) A Disintegrin and Metalloproteinase 10; (i) Pose view of interaction of calotropone with proteins. (ii) Overlay of calotropone in active pockets of proteins|
Click here to view
In this study, the highest docking score was obtained from the interaction between calotropone and Nf-Kβ, suggesting the dominating mechanism of the anticancer activities. The increase level of Nf-Kβ during cancer development and progression is not only exclusive to pancreatic cancer. It is the significance of our findings that calotropone may act as a nonspecific anticancer. Nf-Kβ has a role in the secretion of proinflammatory cytokines and chemokines such as interleukin (IL)-1 β, tumor necrosis factor, and IL-6. The finding in our study can be substantiated by the fact that calotropone exhibited anti-inflammatory properties, which is even higher than ibuprofen.
Molecular docking studies have some limitations attributed to various factors involved in drug interaction in the body. Of which, drug delivery may play a significant part in the treatment efficacy. Our research group have developed several biopolymers which could assist the delivery, such as chitosan,, cellulose,, and pectin. Further studies in-vitro and in-vivo could also be conducted to confirm the drug interaction targeting the Nf-Kβ and other cancer growth-related proteins.
| Conclusions|| |
Our study proved that calotropone has higher docking scores based on its interaction with pancreatic cancer-associated proteins (GCNT3, GOT1, c-Met, PPARγ, BUB1, ADAM10, SOX2, and Nf-Kβ), in comparison with that of gemcitabine. The highest score obtained from calotropone interaction with Nf-Kβ suggests its dominance in the mechanism of action. We further recommend to investigate the role of calotropone in the regulation of Nf-Kβ during the development and progression of cancer cells.
Financial support and sponsorship
Conflicts of interest
There are no conflicts of interest.
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