|
 
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| ORIGINAL ARTICLE |
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| Year : 2021 | Volume
: 5
| Issue : 4 | Page : 446-450 |
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Computational bioprospecting of andrographolide derivatives as potent cyclooxygenase-2 inhibitors
Somdutt Mujwar
Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh, India
| Date of Submission | 07-Apr-2021 |
| Date of Acceptance | 17-Oct-2021 |
| Date of Web Publication | 14-Dec-2021 |
Correspondence Address:
Somdutt Mujwar
Institute of Pharmaceutical Research, GLA University, Mathura - 281 406, Uttar Pradesh
India
 Source of Support: None, Conflict of Interest: None  | 10 |
DOI: 10.4103/bbrj.bbrj_56_21
Background: Inflammation is a protective response of the human body that still causes a high level of discomfort because of the associated pain and other inflammatory reactions. Nonsteroidal anti-inflammatory drugs (NSAIDs) have certain associated severe side-effects such as hepatotoxicity. Thus, there is an urgent need to develop a novel anti-inflammatory agent to counter the associated problems with the existing NSAIDs. Methods: The herbal sources are a very vast treasure for exploring potential leads for the development of novel therapeutic agents to counter the existing healthcare problems for the welfare of humankind. Thus, in the current experimental study, the author has tried to develop some of the novel andrographolide analogs as cyclooxygenase-2 (COX-2) inhibitors by using bioisosteric substitutions. Results: The newly developed andrographolide derivatives have a high affinity for the human COX-2 enzyme, an optimized pharmacokinetic profile as well as being free from any associated toxic effects. Conclusion: The andrographolide derivatives as COX-2 inhibitors are supposed to be free from the side effects associated with NSAIDs with an optimized pharmacokinetic profile.
Keywords: Andrographolide, bioisosteres, cyclooxygenase-2, docking, inflammation
How to cite this article:
Mujwar S. Computational bioprospecting of andrographolide derivatives as potent cyclooxygenase-2 inhibitors. Biomed Biotechnol Res J 2021;5:446-50 |
How to cite this URL:
Mujwar S. Computational bioprospecting of andrographolide derivatives as potent cyclooxygenase-2 inhibitors. Biomed Biotechnol Res J [serial online] 2021 [cited 2023 Jun 9];5:446-50. Available from: https://www.bmbtrj.org/text.asp?2021/5/4/446/332462 |
| Introduction | |  |
Inflammation is a defensive mechanism of the human body involved in the triggering of the pathogenic or host tissue injury. Acute inflammatory response results in the alterations of the local hemodynamics pattern and vascular permeability, causing cellular influx and edema, though the chronic inflammation is involved in the dangerous human diseases such as asthma, cancer, arthritis, neuropsychiatric disorders, and viral diseases.[1] Cyclooxygenase (COX) enzyme is intricate in the biosynthesis of the prostaglandins from arachidonic acid and was involved in the inflammatory reactions. The human COX enzyme exists in the three different isoforms known as COX-1, COX-2, and COX-3.[2],[3] The COX-1 isoform is a housekeeping enzyme involved in the cytoprotective role in the human body by physiological synthesis of the prostaglandins involved in the maintenance of renal and gastric integrity.[3] Inhibition is associated with various gastrointestinal unwanted toxic effects. The use of nonselective COX inhibitors to counter the inflammatory reactions, while the continuous use of nonsteroidal anti-inflammatory drugs such as ibuprofen, naproxen, and indomethacin selectively targeting COX-2 enzymes are having some serious side effects such as nephrotoxicity, gastrointestinal bleeding, and ulceration.[4] Thus, there is an urgent need to explore a newer therapeutic agent targeting COX-2 enzyme as an anti-inflammatory agent to overcome the severe problems associated with the existing anti-inflammatory agents.[5]
The computational methods for designing novel drug molecules were lightning fast and highly economical in nature with very high success rate eliminating the chances of failure at the later stage of drug development. Therefore, these fast approaches are preferred nowadays over the time taking and costly traditional approaches of drug development.[6],[7],[8],[9]
The herbal source is a very vast treasure for exploring potential leads for the development of novel therapeutic agents to counter the existing healthcare problems for the welfare of humankind. Thus, in the current study, some of the diverse herbal leads were explored to identify potential COX-2 inhibitor as an anti-inflammatory agent.[10],[11] The andrographolide is used in the ancient system of medicine for its number of therapeutic efficacies, including anticancer, antimicrobial, and immunomodulatory activity. However, it is having a serious problem of limited bioavailability because of its nonsignificant pharmacokinetic profile.[12] Thus, in the current experimental study, the author has tried to develop some of the novel andrographolide analogs by using bioisosteric substitutions to develop novel leads having high affinity for the human COX-2 enzyme, optimized pharmacokinetic profile as well as free from any associated toxic effects.
| Experimental | | |
Preparation of macromolecule and ligand for docking
The mefenamic acid complexed with human COX-2 enzyme was attained from the RCSB protein databank, and its pdb id was 5IKR.[13],[14],[15] The macromolecular target receptor COX-2 was equipped for performing molecular docking by eradicating the bound ligand from the active site followed by amputation of unwanted water molecules and addition of polar hydrogens.[16] The rotatable, un-rotatable, and nonrotatable bonds were designated for the separated ligand mefenamic acid and were saved in the pdbqt format required by the AutoDock software.[17],[18]
Molecular docking simulation and its validation
The active ligand-binding site of the COX-2 enzyme was recognized by analyzing the interaction residues with the bound mefenamic acid with discovery studio visualizer.[8],[19],[20] The identified active binding site of COX-2 enzyme is to enumerate the grid parameters for the preparation of grid-box to proceed with the docking simulation of COX-2 enzyme.[8],[19],[20],[21] The grid-box covering all the active residues of COX-2 tangled in the binding of mefenamic acid is shown in [Figure 1] and [Figure 2]. | Figure 1: Structural model of human cyclooxygenase-2 complex with mefenamic acid
Click here to view |
 | Figure 2: Grid-box encapsulating the active site present in the macromolecular target cyclooxygenase-2
Click here to view |
The AutoGrid utility present in the AutoDock suite was used to generate atomic map files for various atom types present in the ligand as well as macromolecule. Lamarckian genetic algorithm was utilized by AutoDock as a primary conformational search method to perform molecular docking simulation.[8],[17],[18],[19]
The parameters used to perform molecular docking simulation of the human COX-2 against the reference ligand mefenamic acid was validated by considering the binding energy, chemical interactions as well as overlay of the docked conformation of ligand with respect to its bioactive crystallized conformation.[22],[23]
Ligand library design and virtual screening
In the present study, 152 reported leads from herbal source were utilized to develop a ligand library to screen against the human COX-2 enzyme to identify potential compounds having inhibitory activity. The ligand library consisting of 152 diverse lead molecules from herbal source were virtually screened against the human COX-2 enzyme using computational docking technique to identify their affinity for COX-2 enzyme.[2],[14],[17],[24]
Analogue design
Bioisosteric substitution-based analog design of the shortlisted lead molecule is performed with the intention of improvement of pharmacokinetic profile and increase in the potency of the designed analogs with respect to their parent lead molecule.[23],[25]
ADME and toxicity prediction
The shortlisted lead molecules after performing virtual screening were evaluated for their pharmacokinetic and toxicity profiling. The important physicochemical parameters such as molecular weight (MW), topological polar surface area (TPSA), and calculated partition coefficient (cLogP) were computationally calculated to predict their pharmacokinetic profile on the basis of Lipinski's rule of five. The pharmacokinetic and toxicity profiling of the shortlisted leads was estimated using DataWarrior software.[26],[27],[28],[29]
| Results and Discussion | | |
Preparation of macromolecule and ligand for docking
The structural model of human COX-2 was experimentally resolved by X-ray diffraction technique at a resolution of 2.342Å using Spodoptera frugiperda as expression system. The bound mefenamic acid from the macromolecular complex is separated using software Chimera. The macromolecular complex is having dimeric structure consists of twin polypeptide chains A and B of 551 amino acids each. The chain A was used to perform computational studies while chain B was detached with the help of software Chimera. The macromolecular receptor was prepared for docking by addition of polar hydrogen atoms, removing unwanted water molecules, and the addition and distribution of Gasteiger charge. The processed macromolecular target receptor was saved in pdbqt format of AutoDock software. Three rotatable bonds were present in the ligand, and all of them were kept rotatable for the current experimental study. The prepared ligand was also saved in the pdbqt format of the AutoDock software.
Molecular docking simulation and its validation
Tyr385 and Ser530 are the key residues involved in the active binding of the reference ligand mefenamic acid with the target COX-2 enzyme. Grid box was covering all the active macromolecular residues. The grid coordinates used in the current study were tabulated in [Table 1]. | Table 1: Coordinates used to prepare grid-box for human cyclooxygenase-2 enzyme
Click here to view |
Docking simulation procedure for human COX-2 enzyme was successfully validated as the binding energy of the reference ligand mefenamic acid against the target COX-2 enzyme was observed in the predefined range of-5 to-15 Kcal/Mol. Furthermore, the docked conformation was perfectly overlayed over its bioactive conformation with similar binding interactions. The molecular docking results of the bound ligand mefenamic acid with the human COX-2 receptor are presented in [Table 2]. | Table 2: Results of molecular docking of the reference ligand mefenamic acid against the cyclooxygenase-2 enzyme
Click here to view |
Virtual screening
Virtual screening of 152 diverse lead molecules from herbal source based on the computational molecular docking simulation technique the following five lead molecules were shortlisted on the basis of their binding affinity against the macromolecular target COX-2 enzyme. The results obtained after performing virtual screening are shown in [Table 3]. | Table 3: Binding energy of the shortlisted herbal lead molecules against the human cyclooxygenase-2 enzyme
Click here to view |
Docking studies of analogs
The binding affinity of all the designed analogs was identified after performing virtual screening by analyzing their binding energy obtained for the top-ranking pose of each ligand. The molecular docking results of all the five analog molecules were obtained after performing AutoDock based molecular docking simulation against the human COX 2 receptor shown in [Table 4]. | Table 4: Binding energy of all the designed andrographolide analogue molecules against the human cyclooxygenase-2 enzyme
Click here to view |
The binding interactions of the best andrographolide analog molecules are shown in [Figure 3]. | Figure 3: Binding mode and chemical interactions of the AG2 within the active ligand binding site of cyclooxygenase-2 receptor of human
Click here to view |
Physicochemical properties evaluation
All the designed andrographolide analog molecules were evaluated for their pharmacokinetic profiling by considering parameters such as absorption, distribution, metabolism, and excretion using DataWarrior program. The physicochemical properties responsible for regulating the pharmacokinetic profile of the lead molecules were evaluated by applying Lipinski and Vebar rule. The significant physicochemical properties used in the current study are calculated partition coefficient (cLogP), TPSA, MW, etc. The physicochemical properties of all the four ligand molecules for COX-2 enzyme protein of human are shown in [Table 5]. | Table 5: “Lipinski's rule of five” for the designed andrographolide analog molecules targeting cyclooxygenase-2 enzyme
Click here to view |
ADME and toxicity profiling of lead compounds
The pharmacokinetic profile and toxicity of the designed andrographolide analog molecules were evaluated by DataWarrior software, and the obtained results are tabulated in [Table 6]. All the three newly designed andrographolide analogs were evaluated for the presence of functional groups responsible for major toxic effect, and it was compared with the parent molecule andrographolide as well as the reference molecule mefenamic acid. All the designed andrographolide analog molecules, i.e. AG1, AG2, and AG3 were also found to have an acceptable pharmacokinetic profile but having low drug-likeness score and some serious toxic effects such as mutagenicity, tumorigenicity, and reproductive effects. The Absorption, distribution, metabolism, excretion (ADME) and toxicity results of all the selected ligand molecules are shown in [Table 5] and [Table 6].
| Conclusion | | |
Docking-based virtual screening by AutoDock is very useful in shortlisting potential lead compounds from a diverse ligand library from an herbal source. The andrographolide is found to be the most potent anti-inflammatory agent having potent inhibitory action against the human COX-2 enzyme. The andrographolide is having some bioavailability problems associated with it. Thus, andrographolide analogs were designed by using bioisosteric substitutions with the intent to increase their affinity towards the target COX2 enzyme and remove the associated problems related to the low bioavailability. The obtained in silico results confirm that the andrographolide analog AG2 is having a high affinity toward the target human COX2 enzyme, optimized pharmacokinetic profile with improved bioavailability, and free from any associated toxic effects.
Acknowledgments
The authors are thankful to the management of GLA University, Mathura, for proving all the necessary facilities to complete the work.
Financial support and sponsorship
Nil.
Conflicts of interest
There are no conflicts of interest.
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[Figure 1], [Figure 2], [Figure 3]
[Table 1], [Table 2], [Table 3], [Table 4], [Table 5], [Table 6]
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