Molecular docking studies on phyto-compounds identified from Ruellia tuberosa against cyclooxygenase-1 (PDB ID: 2OYE) and cyclooxygenase-2 (PDB ID: 6COX)
Jul 2026· Research journal of chemistry and environment· Vol 30, pp. 34· 0 citations
TL;DR
The results imply that bioactive substances with strong antiinflammatory potential are present in Ruellia tuberosa and highlight the value of molecular docking as a prediction tool in drug discovery.
Abstract
Computer-Aided drug design (CADD) and in silico
methods have become indispensable tools in
contemporary drug development. Molecular docking is
essential for anticipating how bioactive substances will
interact with target proteins, which makes it easier to
find possible medicinal treatments. In this study,
molecular docking analysis was used to assess the antiinflammatory potential of phytocompounds discovered
from Ruellia tuberosa. Cyclooxygenase-1 (COX-1;
PDB ID: 2OYE) and Cyclooxygenase-2 (COX-2; PDB
ID: 6COX), two important enzymes implicated in
inflammation, were docked against a selection of
phytochemicals including n-hexadecanoic acid, phytol,
9,12-octadecadienoic acid, octadecanoic acid and
squalene. The normal reference medication was
diclofenac. AutoDock Vina was used in docking
research to forecast binding affinities and patterns of
interaction between ligands and target proteins. The
selected phytochemicals exhibited favorable binding
affinities toward COX-1 and COX-2.
The compounds with the highest binding affinity were
squalene, octadecanoic acid and 9,12-octadecadienoic
acid. Hydrophobic and hydrogen bonding interactions
within the target proteins' active site residues were the
main factors stabilizing the connections. These results
imply that bioactive substances with strong antiinflammatory potential are present in Ruellia tuberosa.
The findings support further in vitro and in vivo studies
for the development of novel anti-inflammatory agents
and highlight the value of molecular docking as a
prediction tool in drug discovery.
P predictive findings suggest that specific M. champaca flower constituents possess strong targeted binding potential against PTEN and CXCR4 nodes, establishing a validated computational foundation that warrants downstream in vitro and in vivo functional experimental validation.
Saketh Tenkashala Guruprasad, Karthik Punniyakoddi, V. Karthick et al.· Journal of Computational Bio...· 0 citations
Background: Selective cyclooxygenase-2 (COX - 2) inhibitors reduce gastrointestinal side effects but carry severe complications, promoting the search for safer alternatives from natural sources. Objectives: To identify protein COX - 2 inhibitor through molecular docking - guided virtual screening of phytoconstituents from Physalis minima and subsequent de-novo design of semisynthetic hybrids. Methods: A total of 93 Physalis minima phytoconstituents from the IMPPAT database were screened against the human COX-2 enzyme (5IKR.pdb). Using the top natural lead scaffold, an in silico library of 200 NSAID - caffeic/quinic acid hybrids was designed. Lead candidates were evaluated using MM-GBSA binding energy calculation. SWISS ADME profiling, and a 100 ns molecular dynamic simulation via the Desmond module. Results: Chlorogenic acid (IMPHY0011844) emerged as the top natural lead (binding affinity of -7.8 kcal/mol) from which a 200 in-house NSAID-caffeic acid and NSAID-quinic acid hybrids were designed. From the designed hybrids compound VR6 was evidenced strongest interactions with Arg120, Phe518, Gln192, and Ser530. ADME profiling predicted high gastrointestinal absorption, zero Lipinski violation, and lack of blood -brain barrier penetration. A 100ns molecular dynamics simulation verified that the VR6/5IKR complex exhibited highly stability, maintaining crucial interactions with Arg120 and Ser530 residues. Conclusion: The hybrid molecule VR6 represented a promising, pharmacokinetically sound lead candidate that warrants chemical synthesis and further in vitro biological evaluation as a safer anti-inflammatory therapeutics.
Unknown authors· Genetics and Molecular Resea...· 0 citations
Six previously uncharacterized metabolites isolated from the poisonous mushroom Tricholoma pardinum are investigated using an integrated in silico approach to evaluate their therapeutic potential, highlighting the potential of metabolites from T. pardinum as novel scaffolds for developing anticancer agents targeting PARP1 and PIP4K2γ.
A. Amin, H. M. Amin, A. R. Hamad et al.· Technology and Health Care· 0 citations
The docking analysis suggest that selected N-(substituted-1,3-benzothiazol-2-yl)benzamide derivatives, particularly Cp1, Cp3, Cp7, Cp10, Cp12, Cp13, and Cp14 were identified as the most promising lead candidates, with significant potential for anticonvulsant activity.
A. Rufa'i, A. Idris, A. Musa et al.· Molecular Modeling Connect· 0 citations
Hypertension is a major risk factor for renal and cardiovascular diseases, and angiotensin-converting enzyme (ACE) inhibitors are among the principal therapeutic agents used in its management. This study aimed to predict the ACE-inhibitory activity of unripe C. papaya fruit extract using an in silico approach. GC–MS analysis of the unripe fruit extract indicated the presence of multiple bioactive compounds. Structure-data files for the identified compounds, the standard inhibitor captopril, and ACE complexed with captopril were obtained from PubChem and the Protein Data Bank. The ligand files were converted to PDBQT format for docking. The docking analysis showed binding affinities ranging from −5.8 to −4.1 kcal/mol, while captopril and lisinopril had binding affinities of −5.5 and −7.7 kcal/mol, respectively. Six compounds—cyclooctaneacetic acid, 2-oxo; sucrose; 6,10,14-trimethyl-pentadecan-2-ol; 9,15-octadecadienoic acid, methyl ester, (Z,Z)-; 1-cyclohexylnonene; and [1,4]dioxino[2,3-b]-1,4-dioxin, hexahydro-2,3,6,7-tetramethyl—showed the strongest binding affinities. Similar to the standard drug, these compounds interacted with reported ACE active-site residues, including HIS383, HIS387, GLU384, and GLU411. Pharmacokinetic and toxicity properties were predicted using SwissADME and ProTox-II. The selected compounds showed favourable predicted pharmacological profiles and no predicted hepatotoxicity, immunotoxicity, cytotoxicity, carcinogenicity, or mutagenicity. These findings provide preliminary computational evidence that unripe C. papaya fruit contains constituents with potential ACE-binding activity.
Fatima M. Daura, K. Jaryum, Jonathan D. Dabak et al.· Asian Journal of Biochemistr...· 0 citations
The prevalence of diabetes mellitus is projected to reach 853 million by 2050. Postprandial hyperglycemia induced by the maltase glucoamylase enzyme can exacerbate the condition of diabetic patients. Although acarbose is widely used, it causes gastrointestinal side effects; thus, natural alternatives like ketapang leaves (Terminalia catappa L.) serve as a potential source of antidiabetic active compounds. This study aimed to evaluate the binding affinity, root mean square deviation (RMSD) values, and amino acid interactions of 70 active compounds from ketapang leaves against the maltase-glucoamylase enzyme using a molecular docking approach, alongside designing a novel potential compound modification as an antidiabetic drug candidate. In silico docking simulations were performed using PyRx-AutoDock Vina, structural optimization via VegaZZ, method validation using PyMOL, visualization through Discovery Studio Visualizer, and 2D/3D structural preparation using ChemDraw. The docking results of the 70 test compounds revealed that 41 compounds exhibited ΔGBinding values ranging from -6.3 to -8.5 kcal/mol, 66 compounds showed RMSD values ≤ 2Å, and 5 compounds shared similar amino acid residue interactions with the positive control, acarbose. Structural modification of gallic acid 3-O-(6-galloylglucoside) yielded a novel compound, 4-hydroxy-3-(2-hydroxyethoxy)-5-methoxybenzoic acid, which demonstrated a ΔGBinding value of -5.5 kcal/mol, an RMSD of 1.673 Å, and a matching amino acid residue interaction with the positive control at ASP A:649. In conclusion, active compounds from ketapang leaves and the newly modified compound show promising potential as maltase-glucoamylase enzyme inhibitors via molecular docking.
Unknown authors· Green Health International J...· 0 citations
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