Anti-inflammatory Potential of Quercetin and CAPE in Propolis Against Cyclooxygenase 2 (In silico study)
Budiastuti Budiastuti, Hani Plumeriastuti, Mustofa Helmi Effendi, Vitra Nuraini Helmi, Emmanuel Nnabuike Ugbo, Wiwiek Tyasningsih, Aswin Rafif Khairullah,
Ikechukwu Benjamin Moses
Study Program of Pharmacy Science,
Faculty of Health Science, Universitas Muhammadiyah Surabaya, Indonesia.
*Corresponding Author E-mail: aswinrafif@gmail.com
ABSTRACT:
The prevalence of dental caries worldwide, including in Indonesia, remains very high, demanding more attention due to pulp pain often caused by bacteria. Ibuprofen and aspirin, common nonsteroidal anti-inflammatory drugs (NSAIDs), alleviate pain and inflammation. However, they come with side effects such as digestive tract disorders. To address this issue, in-silico research was conducted to evaluate the potential of propolis, particularly the compounds quercetin and CAPE, as a safer and more effective alternative for treating inflammation and pain. The focus was on their interaction with the enzyme Cyclooxygenase-2 (COX-2). This study aimed to assess the anti-inflammatory activity of quercetin and CAPE compounds against the COX-2 enzyme through in-silico tests. These compounds were analyzed using physicochemical tests, ADMET tests, and PASS tests to predict their biological activity. The results from molecular docking compared the binding strength and stability of quercetin and CAPE to the COX-2 enzyme against the inhibitors ibuprofen and aspirin to determine their potential for better inhibition. Based on the results of physicochemical, ADMET, and PASS tests, quercetin and CAPE are predicted to be promising candidates for anti-inflammatory drugs. Both quercetin and CAPE have shown significant potential as COX-2 enzyme inhibitors in specific molecular docking assays, with binding affinity values of -10 kcal/mol and -9.1 kcal/mol, respectively, as well as hydrogen bond formation to amino acid residues. In conclusion, the research results indicate that quercetin and CAPE from propolis have the potential as anti-inflammatory drugs because they effectively inhibit the activity of the COX-2 enzyme. Further research is needed using in vivo and in vitro models to specifically test the anti-inflammatory effects of quercetin and CAPE compounds in drug formulations.
KEYWORDS: Quercetin, CAPE, Propolis, Anti-inflammatory drugs, COX-2.
INTRODUCTION:
According to WHO, 3.5 billion people in the world experience dental disease. Dental caries is found in all age groups. Caries in untreated, permanent teeth are the highest prevalence dental health problem1-3. There are 2 billion cases of caries in permanent teeth and around 510 million cases of caries in primary teeth.
In Indonesia, the prevalence of caries based on WHO age groups reached 90.2% in the 5-year age group, 72% in the 12-year age group, 68.5% in the 15-year age group, 92.2% in the 35-44-year age group and 95% in the 65+ year age group. As many as 45% of pain cases in the orofacial region are caused by acute pulpitis4.
Pain is a sensory and emotional experience associated with tissue damage, which can interfere with daily activities. Bacterial infections commonly cause pain in the pulp but can also result from trauma, heat, or chemicals. Pulp pain can be relieved with compounds that have analgesic and anti-inflammatory properties One compound that has anti-inflammatory properties is ibuprofen and aspirin5,6. Ibuprofen and aspirin are nonsteroidal anti-inflammatory drugs (NSAIDs) that are often used to reduce pain, inflammation, and fever. These drugs work by inhibiting the enzyme COX, which causes a decrease in the production of prostaglandins from arachidonic acid, a compound that can trigger inflammation and pain7-9. Although generally safe when used in the right doses, ibuprofen can cause side effects in the form of digestive tract disorders. Inhibition of COX-1 also reduces the production of prostaglandins, which can decrease microvascular blood flow, reduce mucus secretion, and increase gastric acid production10.
Propolis is a natural resinous material collected by honeybees from various plants to build and repair their hives. It is made up of approximately 50% vegetable resins and balsams, 30% wax, 10% essential and aromatic oils, and 5% pollen and other substances, including organic matter11. The chemical composition and bioactive properties of propolis can vary based on the bee species, type of source plant, geographical location, and differences in resin composition. Propolis has exhibited various biological activities such as anti-inflammatory, antioxidant, anti-fungal, antiviral, anti-cancer, antimicrobial, antiprotozoal, and antiparasitic effects. It is utilized in traditional medicine, cosmetics, food, and health12. Propolis contains polyphenolic compounds, including flavonoids (such as quercetin) and esters (such as caffeic acid phenethyl ester (CAPE). CAPE, a powerful antioxidant component of propolis, possesses anti-inflammatory, antioxidant, and immunomodulatory properties13,14. Research by Günay et al.15 demonstrated the role of flavonoids and Caffeic Acid Phenylethyl Ester (CAPE) as antioxidants and anti-inflammatories that promote reepithelialization and accelerate the healing process after socket extraction.
COX-2 is an enzyme involved in the synthesis of prostaglandins, which are significant in regulating inflammation, pain, and other physiological processes in the human body16. The various inflammatory mediators involved in pathological processes are prostaglandins (P.G.s), thromboxanes, and leukotrienes. Different prostaglandins are produced through the coordinated activity of the eicosanoid-forming enzyme Cyclooxygenase (COX). Scientific research drives developments aiming to improve the quality of human life and technology17,18. Experimental research methods are categorized into in vivo, in vitro, and in silico19. These terms have Greek origins: in vivo means in life, in vitro means in a glass, and in silico means through computer simulation. In vivo refers to experiments involving whole living organisms, such as animal studies and clinical trials. In vivo tests are often conducted alongside in vitro tests to observe the overall effects of research on living subjects. In vitro refers to research techniques conducted outside the body of an organism in a controlled environment. However, these techniques sometimes struggle to replicate the exact cellular conditions in organisms, especially microbes20. Meanwhile, in silico describes biological research entirely conducted through computers or computer simulations21,22. The term was first introduced by Pedro Miramontes in 1989 at a workshop in Los Alamos, New Mexico.
In silico refers to conducting research and simulations on a computer. This approach is increasingly used in medicine and health, aided by technological advancements and access to extensive databases. In silico studies utilize open and free databases such as DNA and RNA to address medical challenges and advance medical sciences. Bioinformatics plays a key role in identifying new diseases, confirming diagnoses, and developing drugs23. Contemporary drug discovery increasingly relies on computational approaches due to the risks associated with traditional methods24.To evaluate the anti-inflammatory potential of quercetin and CAPE compounds found in propolis, researchers reviewed their specific binding affinity values to the cyclooxygenase 2 enzyme through in silico analysis. These compounds were chosen for their anti-inflammatory effects and high presence in propolis. In silico testing optimizes results from in vitro and in vivo tests25,26. The tests involved physicochemical, molecular docking, ADMET, and PASS tests. Physicochemical tests categorize materials based on their compounds into drug-like or non-drug-like. Molecular docking tests determine binding affinity and the type of bond, ADMET tests profile the pharmacological properties of metabolite compounds, and PASS tests determine the potential activation or inactivation of metabolite compounds27-29.
MATERIALS AND METHODS:
Research Tools:
In this in silico test, researchers used the following tools, applications, and supporting pages: Lenovo brand laptop with an Intel® Core™ i3-10110U CPU @ 2.00 GHz 1.99 GHz processor, 8.00 GB RAM, 64-bit operating system, and Windows 11 operating system with supporting software; PubChem page; RCSB PDB page; The Swiss ADME page; ProTox II website; PASS online page; PyRx App; BIOVIA Discovery Studio Visualizer app.
Research Materials:
In this in silico test, researchers used the following materials to be tested. Quercetin compound CID 5280343 has a 2-dimensional shape in .sdf format and SMILES sequence; Caffeic acid phenyl ester compound CID 5281787 has a 2-dimensional form in .sdf format and SMILES sequence; Macromolecule of cyclooxygenase 2 enzyme with 3-dimensional form in .pdb format. downloaded from protein data bank (www.rcsb.org) with PDB code: 5F19; Ibuprofen compound CID 3672 has a 2-dimensional form in .sdf format and a SMILES sequence; Aspirin compound CID 2244 has a 2-dimensional form in .sdf format and a SMILES sequence.
Research Type and Design:
This research uses a biocomputational approach (in silico). Its design uses an in silico method that consists of physicochemical tests, ADMET, PASS tests, and specific molecular docking. This study was designed to determine and analyze the binding affinity value, Pa > Pi value, and visualization of quercetin and caffeic acid phenyl ester compounds in propolis against COX-2 expression.
Analysis of physicochemical, ADMET, and PASS tests of Quercetine and CAPE compounds:
The physicochemical test results have 5 parameters with varying values. If a test compound fulfills the requirements of each parameter, it can be validated as having drug-like compound characteristics according to the Lipinski Rule of Five. Physicochemical analysis, ADMET, and PASS are carried out by comparing the values and data listed on the relevant testing website with the existing standard values.
Toxicity Test Analysis:
Table 1. Toxicity Test Analysis
|
Parameter Name |
Parameters |
Description |
|
LD50 |
Class I: (LD50 ≤ 5 mg/kg) |
Fatal if swallowed |
|
Class II: (5 < LD50 ≤ 50 mg/kg) |
Fatal if swallowed |
|
|
Class III: (50 < LD50 ≤ 300 mg/kg) |
Toxic if swallowed |
|
|
Class IV: (300 < LD50 ≤ 2000 mg/kg) |
Dangerous if swallowed |
|
|
Class V: (2000 < LD50 ≤ 5000 mg/kg). |
Can be dangerous if swallowed |
|
|
Class VI: (LD50 > 5000 mg/kg). |
Non-toxic |
|
|
Ames Toxicity |
Yes/No |
It aims to determine the mutagenic potential of compounds in silico30 |
|
Skin Sensitisation |
Yes/No |
This test was conducted to determine the sensitivity reaction on the skin in silico30 |
|
Hepatoxicity |
Yes/No |
This test was conducted to determine the toxicity of compounds to the liver in silico30 |
Molecular Docking Analysis Quercetine and CAPE Compounds Against Enzyme COX-2:
The results of the molecular docking test were analyzed based on the binding affinity values using the following conditions: A compound is considered to interact with the target protein if it has a binding affinity value after the molecular docking test31,32; A compound is deemed to be effective if it has a lower binding affinity value compared to the reference compound31; The most optimum value for a compound is at mode zero, upper bound zero, and lower bound zero32,33.
Visual Analysis and Bonding Between Quercetin and CAPE Compounds and Against the Enzyme Cox- 2:
After testing the ligand compound using molecular docking, the compound will be visually analyzed to determine the position and type of bond formed between the test compound and the COX-2 enzyme. The compound must meet the following requirements in order to be considered to have the same bond location: Quercetin and CAPE compounds must coincide or crosslink at a single point in the active site of the cyclooxygenase 2 enzyme34. The compounds quercetin and CAPE must bind to at least one amino acid of cyclooxygenase 235.
RESULT AND DISCUSSION::
Physicochemical Prediction Test Results:
Table 2. Physicochemical test results
|
Compound |
Molecular Mass (Da) |
Hydrogen Bond Donor |
Hydrogen Bond Acceptor |
Log P |
|
Limitations |
≤500 Da |
≤5 |
≤10 |
≤5 |
|
Que* |
302.24 g/mol |
5 |
7 |
-0.56 |
|
CAPE* |
284.31 g/mol |
2 |
4 |
2.62 |
|
IBP* |
206.28 g/mol |
1 |
2 |
3.13 |
|
ASP |
152.15 g/mol |
1 |
3 |
1.21 |
Note: Que: Quercetin; CAPE: Caffeic Acid Phenethyl Ester; IBP: Ibuprofen
The ability of quercetin and CAPE compounds in propolis as anti-inflammatory drug candidates can be assessed from the results of physicochemical tests, ADME prediction, and toxicity. Prediction of physicochemical properties aims to assess the bioavailability of active substances in oral formulations, which is related to the ability of the substance to dissolve and penetrate the digestive tract. Lipinski, after analyzing 2,245 drugs based on data from the World Drugs Index, concluded that compounds that have a molecular weight of more than 500 Da, a log P of more than +5, more than 5 hydrogen bond donors (HBD), and more than 10 hydrogen bond acceptors (HBA) tend to be difficult to absorb and have low permeability. This analysis is known as Lipinski's rule of five because all values are multiples of five36.
Lipinski's rule can be used to assess a compound's hydrophilic/hydrophobic nature, which affects its ability to diffuse through cell membranes passively—the results of predicting the physicochemical parameters of quercetin, CAPE, ibuprofen, and Aspirin. The data in Table 2 indicates that these compounds have physicochemical properties that match at least three or more indicators determined by Lipinski's rule. Therefore, the four compounds have potential as drug candidates based on the Lipinski rule of five requirements37. The physicochemical test results show that the quercetin compound meets the Lipinski requirements because the compound has a molecular mass of 302 Da, hydrogen bond donor 5, hydrogen bond acceptor 7, log P -0.56. Further data from the CAPE compound fulfills the Lipinski requirement because the compound has a molecular mass of 284 Da, hydrogen bond donor 2, hydrogen bond acceptor 4, log P 2.62. While ibuprofen compounds have a molecular mass of 206 Da, hydrogen bond donor 1, hydrogen bond acceptor 2, log P 3.13, they are easily absorbed.
ADMET Prediction Test:
Table 3. ADME prediction test results
|
Components |
Absorption |
Distribution |
Metabolism |
Accession |
|||
|
Water solubility |
Intestinal absorption (human) |
VDss (human) |
BBB permeability |
CNS permeability |
CYP2D6 substrate |
Total Clearance |
|
|
(log mol/L) |
(% Absorbed) |
(log L/kg) |
(log BB) |
(log PS) |
(Yes/No) |
(log ml/min/kg) |
|
|
QUE |
-2.925 |
77.207 |
1.559 |
-1.098 |
-3.065 |
No |
0.407 |
|
CAPE |
-3.031 |
90.637 |
0.139 |
-0.082 |
-2.279 |
No |
0.547 |
|
IBP |
-3.696 |
94.064 |
-0.803 |
0.31 |
-1.695 |
No |
0.263 |
|
ASP |
-1.86 |
76.9 |
-1.7 |
-0.3 |
-2.4 |
No |
0.72 |
The next step in selecting compounds with potential as drug candidates is to perform ADME (Absorption, Distribution, Metabolism, and Excretion) analysis and evaluate their toxicity properties. This is done to reduce the risk of failure in drug development. The utilization of ADMET prediction aims to evaluate drug candidates' safety and oral pharmacokinetic profile. ADME and toxicity properties are assessed through the PKCSM website. Parameters evaluated in the ADMET analysis include HIA scores and water solubility values for absorption, VDss and BBB permeability for distribution, and CYP2D6 and CYP3A4 activities for metabolism and excretion. In addition, carcinogenic and mutagenic potentials were also examined to assess toxicity aspects.
Absorption:
The absorption prediction aims to ensure that the drug candidate is effectively absorbed and permeable in the human body. The HIA value indicates the absorption of the drug in the intestine. Results with HIA values between 0-20% indicate suboptimal absorption, 20-70% indicate moderate absorption, and 70-100% indicate excellent absorption. Both quercetin and CAPE had good absorption, with values of 77% and 90% respectively. The comparison compounds, ibuprofen and aspirin, also demonstrated good absorption with values of 94% and 77% respectively.
Water solubility (log S) indicates how much a molecule can dissolve in water at 25°C. Fat-soluble drugs absorb less than water-soluble drugs, especially if taken enterally. Compounds with water solubility values less than -6 indicate a low level of solubility38. As seen in Table 3, quercetin, CAPE, ibuprofen, and aspirin have water solubility values of -2.9, -3, -3.6, and -1.8, respectively. Therefore, it can be concluded that all four compounds have good absorption ability.
Distribution:
Distribution parameters analyzed include VDss values, blood-brain barrier (BBB) permeability, and central nervous system (CNS) permeability. The volume of Distribution at Steady State (VDss) describes the theoretical volume in which the total dose of the drug must be evenly distributed to reach the same concentration as blood plasma. A higher VDss value indicates that the drug is more dispersed in the tissue than in the plasma. If the VDss value is low, the drug remains in the blood circulation and has low penetration into the tissues. Conversely, if the VDss value is high, the drug leaves the blood circulation and penetrates the tissue with a higher penetration rate. According to Pires et al.36, the VDss value is considered low if the logarithm of VDss is less than -0.15, while it is considered high if the logarithm of VDss is greater than 0.45. As a result of the VDss analysis, quercetin, CAPE, ibuprofen, and Aspirin had log VDss of 1.56, 0.14, -0.8, and -1.7, respectively. The test compounds quercetin and ibuprofen have high VDss values. So, it has a good distribution ability in body tissues. Meanwhile, the VDss value for the CAPE compound is low. Good results on these parameters are good for compounds with low toxicity but potentially dangerous for compounds with high toxicity levels39.
The BBB, or blood-brain barrier, is a parameter used to assess how effectively a drug can cross the brain barrier and reach different areas within the brain. BBB permeability refers to a drug's ability to penetrate the brain, which can help reduce side effects and toxicity risks or increase the drug's effectiveness. The BBB is measured experimentally, and a compound can effectively penetrate the blood-brain barrier if it has a Log B.B. value greater than 0.3. Conversely, compounds with a Log B.B. value of less than -1 are considered poorly distributed. According to Nursanti40, all five test compounds have a low BBB.
If a drug target is located in the dental or oral region and does not directly involve pain signals processed in the brain, COX-2 inhibitor compounds or drugs do not need to penetrate the blood-brain barrier (BBB) to reach their therapeutic target directly. These drugs can exert anti-inflammatory and analgesic effects at the application site or affected area without entering the central nervous system. A good score on this parameter is favorable for compounds with low toxicity but may be risky for compounds with high toxicity.
Metabolism:
The next consideration is the metabolic process. Cytochrome P (CYP) is a vital detoxifying enzyme in the body, mainly present in the liver, which performs oxidation of xenobiotics to facilitate their excretion36. Therefore, assessing the ability of a compound to inhibit cytochrome P is crucial. Cytochrome P plays an important role in the metabolism of many drugs, but inhibition of CYP enzymes can significantly alter the pharmacokinetics of a drug. CYP2D6 and CYP3A4 represented cytochrome P activity in this study. CYP is a type of enzyme that plays a role in the metabolism of endogenous compounds and can catalyze oxidative biological changes in some lipophilic drug compounds and xenobiotics.
The information contained in Table 3 shows that all tested compounds have no inhibitory effect on these enzymes. The derivative compounds will likely be metabolized by these enzymes.
Excretion:
One can measure Total Clearance (CLTOT) to predict compounds' excretion. CLTOT is a combination of hepatic clearance, involving metabolism in the liver and bile, and renal clearance, which is related to excretion through the kidneys. These parameters are linked to bioavailability and are crucial for determining the appropriate dose to achieve steady-state concentrations. From Table 3, the CLTOT values of quercetin are 0.4 ml/min, CAPE is 0.5 ml/min, ibuprofen is 0.26 ml/min, and aspirin is 0.72 ml/min, which can be used to predict the speed of compound excretion. The patient's physiological conditions, such as age, weight, renal function, and liver function, also majorly affect total clearance.
Toxicity test results of compounds with Pro-Tox II and PKCSM:
Table 4. Toxicity test results
|
Compound |
Ames |
LD50 |
Class |
Skin Sensitisation |
|
Quercetin |
Negative |
159 mg/kg |
3 |
No |
|
CAPE |
Negative |
5000 mg/kg |
5 |
No |
|
IBP |
Negative |
299 mg/kg |
3 |
Yes |
|
ASP |
Negative |
250 mg/kg |
3 |
No |
In this study, we conducted toxicity tests to evaluate the potential harm of the compounds we tested. This involved determining LD50 values and toxicity classification using the ProTox II website, as well as mutagenicity testing using the Ames method as predicted through the pkCSM website. The Ames test is a method to assess whether a compound has the potential to cause mutations using bacteria41. Results of this test can be categorized as positive or negative. Positive results indicate that the compound may be mutagenic, potentially a carcinogen, and trigger mutations in cell DNA. On the other hand, negative results indicate that the compound does not have mutagenic properties42. Based on the data in Table 4, we found that quercetin and CAPE compounds, as well as the comparator compounds ibuprofen and aspirin, showed no mutagenic potential.
The next parameter we looked at is the prediction of toxicity as measured by the LD50 (Lethal Dose 50) value. LD50 is the dose that can cause the death of 50% of the experimental animals. LD50 is categorized into six classes: Class 1 (super toxic) for doses < 5 mg/kg, class 2 (extremely toxic) for doses of 5-50 mg/kg, class 3 (highly toxic) for doses of 50-500 mg/kg, class 4 (moderate toxicity) for doses of 0.5-5 g/kg, class 5 (mild toxicity) for doses of 5-15 g/kg, and class 6 (practically non-toxic) for doses > 15 g/kg. According to Table 5, quercetin and ibuprofen are categorized in class 3, while CAPE is in class 5, indicating that these compounds have low acute toxicity effects.
The last parameter we considered is skin sensitization, and we found that both quercetin and CAPE are negative for skin sensitization. This information can be used to set therapeutic doses, drug use doses, and lethal doses before conducting in vitro experiments and in vivo analyses.
PASS Prediction Test Results:
Table 5. PASS prediction test results
|
Compound |
Que* |
CAPE* |
IBP* |
ASP |
|
Pa |
0.689 |
0.544 |
0.901 |
0.762 |
|
Pi |
0.017 |
0.045 |
0.004 |
0.009 |
|
∆P (Pa-Pi) |
0.672 |
0.499 |
0.897 |
0.753 |
Quercetin, CAPE, and ibuprofen compounds were screened to find the most potential compounds as anti-inflammatory agents. The screening was conducted using an online database called PASS Online at the following URL: http://www.way2drug.com/PASSOnline/ , by inputting their respective canonical SMILE. The results of the PASS test provide information on the bioactivity of each compound, including the potential activity (Pa) and potential inhibitory (Pi) values. The PASS Online database can predict over 3500 biological activities, such as pharmacological effects, mechanisms of action, toxicity, side effects, metabolic enzyme interactions, compound involvement in gene expression, and more. The predictions are based on the analysis of approximately 250,000 chemical compound structures, which include drugs, drug candidates, and potentially toxic compounds43,44.
The Pa and Pi values range from 0.000 to 1.000. If the Pa value is above 0.7, the compound has a very high level of biological activity, with results significantly similar to laboratory-scale tests. If the Pa value falls between 0.5 and 0.7, it indicates a good probability of experimental pharmacological action. If the Pa value is less than 0.5, it suggests less chance of experimental activity, but still indicates the potential for discovering new compounds.
The PASS prediction results for quercetin, CAPE, ibuprofen, and aspirin compounds can be seen in Table 5. Based on the results in Table 5, the compounds showed Pa > Pi values of 0.68 > 0.01, 0.54 > 0.04, 0.9 > 0.004, and 0.76 > 0.009, respectively. These values indicate the potential for the compounds to act as active COX-2 enzyme inhibitors. Both quercetin and CAPE have Pa values falling between 0.5 and 0.7, indicating a fairly high level of biological activity, making them bioactive substances in experimental tests and suggesting potential for development as new drug compounds with related bioactivity45.
Molecular Docking Test Results:
Molecular docking results of quercetin, CAPE from propolis, and comparator compounds ibuprofen and aspirin against COX-2 by specific docking.
Table 6. Molecular docking test results
|
Target |
Compounds |
Binding affinity (kcal/mol) |
Mode |
RSMD |
|
|
Lower bound |
Upper bound |
||||
|
COX-2 |
Quercetin |
-10.0 |
1 |
0 |
0 |
|
CAPE |
-9.1 |
1 |
0 |
0 |
|
|
Ibuprofen |
-7.4 |
1 |
0 |
0 |
|
|
Aspirin |
-6.3 |
1 |
0 |
0 |
|
Visualization
Figure 1. Visualization of the bonds formed between quercetin (a), CAPE (b), and the comparator compounds ibuprofen (c) and Aspirin (d) against COX-2.
Table 7. Bond visualization results
|
Target Protein |
Ligand |
Bond Type |
Amino Acids |
|
COX-2 |
Quercetin |
Hydrogen |
Leu531, Met522, Phe 209, Leu531, Leu 534 |
|
Hydrophobic |
Ala527, Leu534, Val349, Ala527, Gly526, Phe381,Ala527, Leu534 |
||
|
Cape |
Hydrogen |
Leu531, |
|
|
Hydrophobic |
Val523, Phe381, Leu352, Ala527, Leu534 |
||
|
Ibuprofen |
Hydrogen |
Leu531, Tyr385, |
|
|
Hydrophobic |
Val523, Ala527, Leu352, Val523, Phe518, Val349 |
||
|
Aspirin |
Hydrogen |
Tyr385, Leu531 |
|
|
Hydrophobic |
Ala527, Val349, Leu531 |
A method that can be applied to find new drug candidates from plant metabolite compounds is in silico studies using molecular docking simulations. Molecular docking simulation allows us to evaluate the interaction between the tested compounds and receptors in the human body. Molecular docking tests can provide information through interactions of metabolite compounds that act as ligands with receptors in the human body. In this in silico study, molecular docking simulation of quercetin and CAPE compounds derived from propolis with target receptor in the form of COX-2 enzyme with PDB ID 5F19 was conducted. The COX-2 enzyme represented by the PDB ID has a resolution of about 2.04 Å and is derived from homo sapiens or human organisms. The smaller the resolution value, the higher the quality of the receptor crystal resolution so that the structural representation will be closer to the original structure46.
Molecular docking evaluated the binding affinity between the test compound and the COX-2 enzyme. This process begins with determining the position and size of the grid box to be used through the validation stage. This grid box aims to determine the receptor area at x, y, and z coordinates to identify the ligand's lowest energy conformation. The smaller the RMSD value (≤ 2) and the bond energy generated by the grid box, the more valid the repairing results are47. The RMSD value is measured from the superposition between the original ligand and the redocking result. It is used to evaluate the accuracy of the computational method in the experimental procedure. After determining the appropriate grid box size and position, molecular docking was performed on test compounds such as quercetin, CAPE, and ibuprofen as comparison ligands and aspirin as native ligands. Aspirin is a non-steroidal anti-inflammatory drug with analgesic, antipyretic, and anti-inflammatory effects.
The parameters analyzed in molecular docking include the number of hydrogen bonds, binding affinity value, and RMSD as noted by Arwansyah et al.48. These parameters affect the ligand's ability to bind to the receptor. The formation of more hydrogen bonds between the test ligand and the native ligand increases the likelihood of the test compound inhibiting the activity of the target protein or receptor by displacing the native ligand. Lower or negative binding affinity values indicate potential bond formation between the ligand and macromolecules49.
In the docking results on COX-2, there are differences in binding affinity values between quercetin, CAPE, ibuprofen, and aspirin compounds. The level of binding affinity indicates the strength of the affinity of quercetin and CAPE to COX-2; the lower the binding energy, the more stable the bond formed50. The binding affinity value of quercetin with COX-2 is -10.0 kcal/mol, while CAPE with COX-2 is -9.1 kcal/mol, ibuprofen with COX-2 is -7.2 kcal/mol, and aspirin with COX-2 is -6.3 kcal/mol. The molecular docking test results (Table 6) indicate that quercetin and CAPE compounds in propolis have good COX-2 inhibitor ability due to their lower binding affinity values compared to ibuprofen and aspirin. This suggests that the quercetin and CAPE compounds in propolis can be effective anti-inflammatory agents because they can outcompete the formation of bonds between ibuprofen and aspirin, which are common anti-inflammatory drugs, at the active site of cyclooxygenase 251.
In addition to considering binding affinity, the value of RMSD, as noted by Du et al.52, is also crucial to note. Both quercetin and CAPE from propolis and comparison compounds have lower and upper limit RMSD values of 0, indicating high accuracy. Visualization using Discovery Studio 2020 Client software was then performed to display the docking results in 2D and 3D. It can visualize molecular docking results, including the amino acids that serve as the location of ligand tethering on the receptor protein. The observed interactions include hydrogen bonds, hydrophobic interactions, and electrostatic interactions within the tethering region with a distance of less than 5 angstroms (<5Å). Hydrogen bonding, as noted by Fu et al.53, affects protein stability and occurs through interactions between covalently bound hydrogen atoms and electronegative atoms such as fluorine (F), nitrogen (N), and oxygen (O)54.
The visualization of the quercetin compound revealed the formation of hydrogen bonds at amino acids LEU531, MET522, PHE 209, LEU531, and LEU 534, reinforced by several hydrophobic interactions at amino acids ALA527, LEU534, VAL349, ALA527, GLY526, PHE381, ALA527, LEU534. Similarly, the visualization of the CAPE compound indicated the formation of hydrogen bonds at LEU531, supplemented by hydrophobic interactions at amino acids VAL523, PHE381, LEU352, ALA527, and LEU534.
The results of the molecular docking test showed that quercetin and CAPE in propolis exhibit similar molecular activity to the original ligand, aspirin, as both compounds share identical peptide binding sites at the active site of the COX-2 enzyme55. Consequently, both compounds demonstrate strong anti-inflammatory potential. Furthermore, the test ligands or compounds display the same binding site at LEU531 (LEUSIN 531) and the same hydrophobic bond at ALA527 (ALANIN 527) superimposed on the same orbital pocket. This similarity in binding sites suggests that the bound proteins possess similar properties, resulting in comparable binding affinity values and interaction modes. The existence of similar binding sites and low binding affinity of the test compounds also implies the potential of the compounds as competitive inhibitors of the COX-2 enzyme56,57.
CONCLUSION:
The compounds quercetin and CAPE, which are found in propolis, have been identified as potential drug candidates. They have undergone physicochemical tests, ADME analysis, and toxicity prediction. These compounds have shown specific potential for inhibiting the COX-2 enzyme based on PASS prediction, docking-specific assay, and visualization. As a result, quercetin and CAPE from propolis show promise as anti-inflammatory drugs due to their ability to effectively inhibit the activity of the COX-2 enzyme. Further research using in vivo and in vitro models can be carried out to test the anti-inflammatory effects of these compounds in drug formulations derived from propolis. This data can be used as a reference for the potential development of anti-inflammatory drugs utilizing quercetin and CAPE.
CONFLICT OF INTEREST:
The authors have no conflicts of interest regarding this investigation.
ACKNOWLEDGMENTS:
This study was partly supported by The International Research Consortium, Lembaga Penelitian dan Pengabdian Masyarakat, Universitas Airlangga, Surabaya, Indonesia in year 2024 with grant number: 171/UN3.LPPM/PT.01.03/2024.
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Received on 30.10.2024 Revised on 19.02.2025 Accepted on 21.05.2025 Published on 08.11.2025 Available online from November 13, 2025 Research J. Pharmacy and Technology. 2025;18(11):5320-5328. DOI: 10.52711/0974-360X.2025.00767 © RJPT All right reserved
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