Molecular Docking Studies of Nigella Sativa Linn Seed Compound Against Alzheimer's Disease: An in silico Study

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Published: 2024-03-22

Page: 32-42

S. Sudha

Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.

B. Chitra

Department of Biotechnology, Srimad Andavan Arts and Science College (Autonomous), Affiliated to Bharathidasan University, Tiruchirappalli, Tamil Nadu, India.

S. Arif Nisha *

Regional Forensic Science Laboratory, Race Course Road, Kaja Nagar, Edamalaipatti Pudur, Tiruchirappalli, Tamil Nadu, India.

R. Beema Shafreen

Dr. Umayal Ramanathan College for Women, Affiliated to Alagappa University, Alagappapuram, Karaikudi, Tamil Nadu, India.

*Author to whom correspondence should be addressed.


Alzheimer's disease is a neurological disorder that can lead to brain atrophy and dementia, affecting cognitive, social, behavioral, and emotional abilities. Medicinal plants have proven to be effective in addressing Alzheimer's disease. Nigella sativa Linn seeds have been extensively utilized in managing a range of nervous system conditions, including AD, epilepsy and neurotoxicity. In this study, it has been reported that the evaluation of the anti-Alzheimer potential of phytoconstituents in Nigella sativa Linn seeds was done using molecular docking analysis.            The AutoDock 4.2.6 software has used the chemical Kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside) to identify and fulfill the Lamarckian genetic algorithm. The binding affinity of Kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside) with key targets: acetylcholinesterase, amyloid beta peptide, and beta-secretase, represented by PDB IDs 7E3H, 2M4J, and 1FKN, respectively. Remarkably, Nigella sativa L., seeds exhibit a superior binding affinity and inhibitory effect on acetylcholinesterase (AChE), amyloid beta peptide (Aβ or APP) and beta-secretase (BACE) compared to conventional medication. Donepezil was employed as a positive control in this investigation. This study delves into the evaluation of Nigella sativa Linn's phytoconstituents for their potential in combating Alzheimer's disease through molecular docking analysis. Among the bioactive components of Nigella sativa Linn, kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside) and the standard drug Donepezil stand out as promising candidates for therapeutic purposes. The affinity of Kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside (Binding energy = -7.84 kcal/mol) to bind with acetylcholine esterase significantly surpasses that of the standard drug Donepezil, as indicated by the higher binding energy. The ligand efficiency of Kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside, calculated as the binding energy per non-hydrogen atom (-0.37 kcal/mol), is also greater than that of the standard drug Donepezil. These findings underscore the importance of further comprehensive research on Kaempferol 3-(2-galloyl-alpha-L-arabinopyranoside) as a potential treatment for Alzheimer's disease, owing to its superior efficacy compared to existing medications.

Keywords: Kaempferol 3-(2"-galloyl-alpha-L-arabinopyranoside), donepezil, Alzheimer's disease, in silico, Nigella sativa Linn, Molecular docking

How to Cite

Sudha, S., Chitra, B., Nisha , S. A., & Shafreen, R. B. (2024). Molecular Docking Studies of Nigella Sativa Linn Seed Compound Against Alzheimer’s Disease: An in silico Study. Asian Journal of Advances in Medical Science, 6(1), 32–42. Retrieved from


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