COX-2 as a Therapeutic Target:
An in Silico Approach to Indole Alkaloids for Analgesic Discovery
Swati Jain1, Sukhwant Singh2
1Faculty of Pharmaceutical Sciences, Sanjeev Agrawal Global Educational University, Bhopal,
Madhya Pradesh, India.
2Sagar Institute of Research and Technology – Pharmacy, Sanjeev Agrawal Global Educational University, Bhopal, Madhya Pradesh, India.
*Corresponding Author E-mail: jain.swati71289@gmail.com, singh.sukhwant@gmail.com
ABSTRACT:
Pain is a complex physiological process that involves the activation of nociceptors and transmission of pain signals to the brain. COX-2 (Cyclooxygenase-2) is an inducible enzyme that plays a key role in the inflammatory process by converting arachidonic acid into prostaglandins, particularly PGE2, which sensitizes nociceptors and leads to pain perception. Inhibiting COX-2 can reduce inflammation and pain, making it a significant target for drug discovery. This study utilizes computational approaches to explore the binding interactions of natural compounds with COX-2 (PDB ID: 4COX) using molecular docking. Ajmalicin forms van der Waals interactions with residues like VAL:116 and hydrogen bonds with ARG:120 and TYR:355, ensuring strong stability in the binding site. Vellosimine and Vellosiminol exhibit similar interaction profiles, primarily engaging hydrophobic and aromatic residues through van der Waals and Pi-alkyl interactions. Vinorine, the focus of the table, binds extensively to COX-2 through van der Waals and Pi-alkyl interactions with residues such as LEU A:531, MET A:522, and PHE A:518, stabilizing its position within the hydrophobic binding pocket. These natural compounds show potential as COX-2 inhibitors, offering avenues for developing new anti-inflammatory agents.
KEYWORDS: Pain, COX-2 inhibition, Molecular docking, Ajmalicin, Vinorine, Anti-inflammatory agents.
INTRODUCTION:
Pain is a complex physiological process involving sensory, emotional, and cognitive components. It begins with the activation of nociceptors, which are specialized nerve endings that detect harmful stimuli like injury or inflammation. These signals travel through peripheral nerves to the spinal cord and brain, where they are processed and interpreted as pain. The brain's response involves multiple regions, including the somatosensory cortex, which identifies pain location and intensity, and the limbic system, which links it to emotions.1,2
Various neurotransmitters, such as glutamate and substance P, facilitate pain transmission, while endogenous opioids and other modulators help regulate and inhibit pain perception. COX-2 (cyclooxygenase-2) is an enzyme primarily induced during inflammation and plays a key role in pain. It converts arachidonic acid into prostaglandins, particularly PGE2, which are mediators that sensitize nociceptors, leading to pain perception.3,4 COX-2 expression increases in response to tissue injury, inflammation, and other stimuli, contributing to both acute and chronic pain states. Elevated prostaglandin levels amplify the pain signal transmission in peripheral nerves and central nervous system pathways. Inhibiting COX-2 with nonsteroidal anti-inflammatory drugs (NSAIDs) reduces prostaglandin production, thereby decreasing pain and inflammation, making COX-2 a crucial target in pain management strategies. Computational approaches in drug discovery utilize advanced algorithms, molecular modeling, and bioinformatics to identify and optimize potential drug candidates.5,6 Computational approaches in discovering COX-2 inhibitors from natural products involve virtual screening of natural compound libraries, molecular docking to predict binding affinities, and molecular modeling to identify structural features important for COX-2 inhibition.7,8 Molecular dynamics simulations assess the stability of inhibitor-enzyme complexes. These methods streamline the identification and optimization of potential COX-2 inhibitors, accelerating natural product-based drug discovery.
EXPERIMENTAL:
Docking Protocol:
Molecular docking investigations was performed on selected phytochemicals against COX-2. The molecular structures of these phytochemicals were sourced from PubChem, while the COX-2 [PBD ID: 4COX] was downloaded from the Protein Data Bank (PDB) at www.rcsb.org/pdb. Pre-processing steps involved editing the COX-2, including the removal of heteroatoms and addition of C-terminal oxygen. Gasteiger Marsili partial charges were assigned to ligands, non-polar hydrogen atoms were merged, and torsions were allowed during docking.9 Active pockets were identified using LIGPLOT, and the Computed Atlas of Surface Topography of Proteins server verified these pockets. Docking employed the Lamarckian Genetic Algorithm for energy minimization with default parameters, and Discovery Studio was employed for result visualization.
RESULTS:
Ajmalicin forms strong van der Waals interactions with residues like VAL:116, HIS:90, and LEU:359, which are crucial for stabilizing the compound within the COX-2 binding pocket. It also participates in conventional hydrogen bonding with residues like ARG:120 and TYR:355, reinforcing its position. SER:530 forms a carbon hydrogen bond with Ajmalicin, adding more stability. Interactions with hydrophobic residues such as LEU:352 and ALA:527 through alkyl and Pi-alkyl contacts also play a vital role in strengthening its binding affinity. Vellosimine primarily interacts with COX-2 through van der Waals interactions with residues such as GLY:526, LEU:352, and PHE:518. It also engages in Pi-alkyl interactions with residues like TRP:387 and TYR:385, indicating a preference for aromatic residues. These interactions are further stabilized by a carbon hydrogen bond with SER:530, ensuring a tight fit in the binding site. The engagement with both polar and nonpolar residues reflects a balanced interaction profile.
Table 1: Docking Interaction of Indole alkaloids B with COX-2
|
Compound |
Van der Waals |
Conventional Hydrogen Bond |
Carbon Hydrogen Bond |
Pi-Sigma |
Alkyl |
|
Ajmalicin |
VAL:116, HIS:90, LEU:359, ARG:513, GLN:192, ILE:517, SER:530, LEU:531 |
ARG:120, TYR:355 |
|
SER:353 |
VAL:349, ALA:516, ALA:527, LEU:352 |
|
Alstoyunine G |
SER 353, PHE 518, LEU 352, PHE 381, LEU 531, LEU 534 |
SER 530 |
GLY 526 |
|
|
|
Alstoyunine H |
SER 353, PHE 518, LEU 352, LEU 359, LEU 531 |
GLY 526 |
|
|
|
|
Vellosimine |
GLY 526, MET 522, LEU 352, PHE 518, TYR 348, LEU 359, SER 353, LEU 352 |
SER 530, VAL 523 |
|
ALA 527 |
|
|
Vellosiminol |
VAL A:523, VAL A:349, LEU A:359, LEU A:352, PHE A:518, PHE A:381, TRP A:387, LEU A:384, ARG A:513, HIS A:90 |
TYR A:355 |
SER A:530 |
GLY A:526 |
|
|
Vinorine |
LEU A:531, LEU A:352, GLY A:526, ALA A:527, LEU A:359, VAL A:349, ARG A:120, TYR A:355, SER A:353 |
SER A:530 |
|
|
VAL A:523, LEU A:384 |
Table 1: Continue
|
Compound |
Pi-Alkyl |
Pi-Sulfur |
Pi-Pi T-shaped |
Amide-Pi Stacked |
Alkyl |
Pi-Alkyl |
|
Ajmalicin |
VAL:523, PHE:518 |
|
|
|
|
|
|
Alstoyunine G |
|
MET 522 |
TRP 387, TYR 385 |
VAL 523, VAL 349 |
LEU 384 |
LEU 384, LEU 531 |
|
Alstoyunine H |
|
MET 522 |
TRP 387, TYR 385, HIS 90 |
|
LEU 384, VAL 523 |
LEU 384, LEU 531 |
|
Vellosimine |
|
|
|
|
VAL 349, LEU 384 |
TRP 387, TYR 385, ALA 527 |
|
Vellosiminol |
|
MET A:522 |
TRP A:387 |
|
|
|
|
Vinorine |
MET A:522, PHE A:518, PHE A:381, TYR A:385, TRP A:387 |
|
|
|
|
|
Vellosiminol shows a similar interaction pattern to Vellosimine, with van der Waals interactions involving residues like VAL A:523, VAL A:349, and PHE A:518. TYR A:355 forms a conventional hydrogen bond, contributing to ligand stabilization. Pi-alkyl interactions with MET A:522 and Pi-sigma interactions with GLY A:526 further enhance the compound’s binding strength by engaging aromatic residues and sulfur-containing groups. These multiple interactions highlight a diverse binding mode, engaging both hydrophobic and polar residues. Vinorine binds COX-2 through extensive van der Waals interactions with residues such as LEU A:531, LEU A:352, and VAL A:349, which stabilize the molecule within the hydrophobic region of the binding pocket. A carbon hydrogen bond is observed with SER A:530, while Pi-alkyl interactions with residues like MET A:522 and PHE A:518 contribute to further stabilization, especially with aromatic and hydrophobic residues. This combination of interactions makes Vinorine a well-stabilized ligand.
Figure 1: Docking Interaction of Ajmalicin with COX-2
Figure 2: Docking Interaction of Alstoyunine G with COX-2.
Figure 3: Docking Interaction of Alstoyunine H with COX-2.
Figure 4: Docking Interaction of Vellosimine with COX-2.
Figure 5: Docking Interaction of Alstoyunine H with COX-2.
Figure 6: Docking Interaction of Vinorinewith COX-2.
Vellosiminol likely follows a similar interaction pattern, utilizing a combination of van der Waals forces, hydrogen bonds, and Pi-alkyl interactions. Hydrophobic residues like LEU and VAL are critical for its positioning within the COX-2 active site, while aromatic residues likely facilitate Pi-interactions. Similar to the other compounds, Vinorine engages with the COX-2 enzyme through a mix of van der Waals interactions with residues such as LEU, VAL, and SER. It may also form hydrogen bonds with residues like TYR or ARG, and Pi-alkyl interactions could stabilize the compound by engaging aromatic residues like TRP or PHE.
DISCUSSION:
The docking interactions of the compounds Ajmalicin, Vellosimine, Vellosiminol, and Vinorine with the COX-2 enzyme provide valuable insights into their potential mechanisms of inhibition. COX-2 (Cyclooxygenase-2) is an enzyme involved in the production of prostaglandins, which mediate inflammation (5,10,11). Understanding how these compounds interact with the COX-2 binding site (PDB ID: 4COX) can shed light on their anti-inflammatory potential (12,13). Ajmalicin interacts strongly with the COX-2 active site through van der Waals interactions with residues like VAL:116, HIS:90, and LEU:359, all of which contribute to its stable positioning within the hydrophobic region of the active site. This is crucial, as these residues are part of the enzyme's hydrophobic pocket that helps stabilize ligands. The conventional hydrogen bonds formed with ARG:120 and TYR:355 further anchor Ajmalicin within the active site, ensuring specificity and enhanced binding affinity. SER:530 provides an additional stabilizing interaction via a carbon hydrogen bond. Vellosimine shows a strong interaction profile with COX-2, engaging van der Waals forces with residues such as GLY:526, LEU:352, and PHE:518. These residues are part of the enzyme's catalytic domain, and their engagement indicates a significant inhibitory potential for Vellosimine. The compound's Pi-alkyl interactions with aromatic residues such as TRP:387 and TYR:385 enhance its stabilization in the binding pocket, reflecting the importance of aromatic stacking interactions in ligand binding. Vellosiminol exhibits an interaction pattern akin to Vellosimine, interacting through van der Waals forces with residues like VAL A:523, VAL A:349, and PHE A:518. Its hydrogen bond with TYR A:355 suggests a firm anchoring within the active site, contributing to its ligand stabilization. Pi-alkyl interactions with MET A:522 and Pi-sigma interactions with GLY A:526 add further strength to the binding by engaging aromatic and sulfur-containing residues. Vinorine binds COX-2 extensively through van der Waals interactions with residues like LEU A:531, LEU A:352, and VAL A:349, effectively positioning the compound within the enzyme’s hydrophobic pocket. The carbon hydrogen bond formed with SER A:530 contributes to its enhanced stability, while Pi-alkyl interactions with MET A:522 and PHE A:518 highlight the importance of hydrophobic and aromatic stacking interactions for ligand binding. All compounds exhibit a combination of van der Waals forces, hydrogen bonding, and Pi-alkyl interactions within the COX-2 binding site. The residues involved, including LEU:352, VAL:349, and SER:530, are crucial components of the hydrophobic pocket, catalytic region, and hydrogen-bonding network of COX-2. The consistent interaction of these compounds with SER:530 highlights the importance of this residue in stabilizing ligands within the active site, as it is located in a key region of the enzyme’s binding pocketThis comprehensive binding profile suggests that these compounds have a strong affinity for the COX-2 active site and could potentially act as inhibitors by blocking access to the catalytic site, preventing the enzyme from producing pro-inflammatory prostaglandins (6,14). As such, Ajmalicin, Vellosimine, Vellosiminol, and Vinorine present promising avenues for the development of COX-2 selective inhibitors with potential anti-inflammatory effects.
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Received on 30.07.2024 Revised on 23.11.2024 Accepted on 28.01.2025 Published on 01.07.2025 Available online from July 05, 2025 Research J. Pharmacy and Technology. 2025;18(7):3302-3306. DOI: 10.52711/0974-360X.2025.00477 © RJPT All right reserved
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