In-Silico Investigational Study of Pyrido-acridine Congener Amphimedine against Alzheimer’s Disease

 

Dipanjan Karati*

Department of Pharmaceutical Technology, Techno India University, West Bengal, Kolkata-700091, India.

*Corresponding Author E-mail: karatibabai@gmail.com

 

 

ABSTRACT:

Aims: To investigate in-silico result of potent phytocomponent amphimedine against Alzheimer’s disease as Glycogen synthase kinase-3 inhibitor. Background: The neurodegenerative illnesses Parkinson's disease (PD) and Alzheimer's disease (AD) have become two of the most significant health issues of the twenty-first century. The drugs currently used to treat AD and PD are ineffective and have side effects. One of the most important and conservative sources of medications for treating neurological issues is natural goods.
Objective: A Pyrido-acridines congener is amphimedine. However, a thorough investigation into amphimedine's impact on AD has yet to be conducted. Numerous in silico investigations, beginning with molecular docking against glycogen synthase kinase-3 for AD, were performed to assess the neuroprotective impact of amphimedine. Utilizing the software Auto Dock 4.1, the results were contrasted with those of three conventional medications. Amphimedine's physiochemical characteristics, including the Lipinski rule of five, drug-likeness, and factors like its absorption, distribution, metabolism, elimination, and toxicity (ADMET) profiles, were also investigated. With acceptable ADMET profiles for therapeutic usage, Amphimedine conforms to all five of Lipinski's parameter. Method: Autodock tools carried out the docking investigation. On the RCSB website, the necessary proteins have been downloaded. The ProTox-II service projected its toxicity category.
Result: The phytocompound has strong affinityfor 1Q5K as GSK-3 blocker. The molecule's toxicology has been examined. As a result, we now recognize that this scaffold solely exhibits immunotoxicity and falls into toxicity class 4. Conclusion: In comparison to currently prescribed standard medications, the docking results (kcal/mol) demonstrated relatively better effectiveness against AD-related targets. Overall, molecular docking's potential binding affinity and additional multiparametric drug-ability profiles imply that amphimedine might be a good therapeutic lead for treating AD. However, employing amphimedine as a prospective medicine against AD treatment requires more clinical and in vivo investigations, where the in-silico data are more beneficial to speed up drug design.

 

KEYWORDS: Amphimedine, Alzheimer’s disease, In silico, Lipinski’s rule, Drug-likeness, Glycogen synthase kinase-3.

 

 

 


1. INTRODUCTION:

A long-established and comprehensive method of treating illness and injury is traditional Chinese medicine (TCM). Before the development of contemporary Western medicine, TCM was the most widely used form of healthcare in eastern Asia. Acupuncture and TCM are still utilized to address human health issues in China and other nations, including Chinese herbal medicine1-5. Treating chronic diseases with herbal medicines has attracted much attention from researchers worldwide in recent years due to its broad range of biological activity and minimal side effects. Due to its excellent biological efficiency and minimal side effects, traditional Chinese medicine has recently gained worldwide appeal. Due to its proven curative properties and potential safety issues, Chinese herbal medicine has a long history of use in China and has sparked significant study interest globally6. Alzheimer's disease (AD) is the utmost common type of neurodegenerative disorder, categorized by successive memory loss. Deposition of amyloid protein and formation of intracellular neurofibrillary tangles are pathological indications of AD. This is a progressive neurodegenerative condition that mostly affects the elderly and is characterized by chronic neuroinflammation, amyloid-beta (Aβ) deposition and formation of neurofibrillary tangles of tau proteins in the brain parenchyma.7-11. The widely recognized regulator glycogen synthase kinase-3 (GSK-3) is involved in the development and subsequent progression of the pathophysiology of AD and regulates a number of crucial targets related to neuronal degeneration. GSK-3 inhibition has neuroprotective benefits, lowers β-amyloid formation, and lowers tau hyperphosphorylation, all of which are linked to AD. The first GSK-3 inhibitor used for therapeutic purposes was lithium, which has been used for a long time with excellent success. Strong GSK-3 blockers with a wide range of structural variations have been discovered recently12-21.

 

Pyridoacridine has aromatic and alkaloid components that have been shown to have the ability to prevent cancer cell growth as a bioactive chemical from a marine organism22–24. The isolation and structure determination of marine alkaloids, which are biologically active, based on some of these isomers sparked interest in "pyridoacridines," or tetracyclic systems in which a pyridine ring is fused to an acridine. There are fifteen isomers of these compounds25. In the process of developing new drugs, natural products are extremely important. To evaluate the anti-Alzheimer potential of medicines or chemicals, several in vitro, in vivo, and computational methodologies were used. Among these methods, docking has been used widely in drug designing for AD. Here, we have selected Amphimedine (Pyrido-acridine congeners) (Figure 1) for in-silico study to investigate it as potent anti-Alzheimer agents via gsk-3 inhibition.

 

 

10-methyl-8H-benzo[b]pyrido[4,3,2-de][1,8]phenanthroline-8,11(10H)-dione

Figure 1. Pyrido-acridine Congeners (Amphimedine)

2. METHODOLOGY:

2.1 Ligand and protein 

The 3-dimensional (3D) structure of amphimedine was designed by chemdraw software. The GSK-3 antagonist protein (PDB ID 1Q5K) with 1.94 Å resolution was downloaded from the protein data bank (http://www.rcsb.org)26-31.

 

2.2 The ligand’s toxicological scheme:

While choosing a drug component, it's crucial to consider the compound's lethality. Here, the poisonousness of Pyrido-acridines (table 3) were enumerated by the ProTox-II tool32.

 

3. RESULTS:

3.1 In Silico Results of Amphimedine against AD:

Autodock-vina was used to investigate in-silico study of amphimedine with 1Q5K. The polar hydrogen and Kollman partial atomic charge were assigned to TLR4/MD-2 complex by using AutoDock4 software (v 4.2.6). The grid dimension was x = 24.262, y = 42.286, z = 21.070. The outcome from this docking was later analysed by using Auto Dock Vina Tools software. The auspicious docked recording poses as ascertained by Auto Dock tool was approved and exposed by Biovia Discovery Studio Visualizer.

 

3.2 Docking against pdb id: 1Q5K for Amphimedine:

The 3D and 2D representations of phytocompound and the three standard drugs have been embodied by the subsequent figures 2, 3, 4, 5, 6, 7, 8, and 9. The individual ligands docking score against individual targets were recorded in Table 1. As per the Auto Dock software, the docking score is always expressed in a negative value, where a higher negative value indicates a better potency.

 

 

Figure 2. 3D representation of ligand binding

 

Figure 3. 2D representation of ligand binding

 

 

Figure 4. 3D representation of Donepezil

 

 

 

Figure 5. 2D representation of Donepezil

 

 

 

 

 

 

 

 

Docking against pdb id: 1Q5K for Galantamine:

 

Figure 6. 3D representation of Galantamine          

 

 

Figure 7. 2D representation of Galantamine

 

Docking against pdb id: 1Q5K for Rivastigmine

 

Figure 8. 3D representation of Rivastigmine

 

Figure 9. 2D representation of Rivastigmine

 

Table 1. Binding energy of phytocompound and the standard three drug molecules

Amphimedine/Standard

GSK-3 (PDB ID: 1Q5K)

Amphimedine

-9.9 Kcal/mol

Donepezil

-8.6 Kcal/mol

Galantamine

-7.6 Kcal/mol

Rivastigmine

-6.4 kcal/mol

 

3.3 Lipinski’s analysis:

The phytocompound was studied according to Lipinski parameters (Table 2).

 

Table 2. Lipinski study of amphimedine.

Parameters

Values

LogP (<5)

2.70

MW (≤500)

313.32

Hydrogen bond acceptor (≤10)

5

Hydrogen Bond donar (≤5)

0

Violation

0

 

3.4 Toxicity analysis:

The phytocompound (amphimedine) was evaluated for its noxiousness. One of the essential therapeutic belongings of a scaffold is its safety. Consequently, the evaluation of toxicity supports to eliminatelethal ligands. The toxic profile of molecules is alienated into six diverse categories (figure 10).

 

 

Figure 10. Category of toxicity

 

Table 3: Evaluation of toxicity, toxicity class, and toxicity status of ligands.

Toxicity

Response

Hepatotoxicity

Negative

Mutagenicity

Negative

Carcinogenicity

Negative

Cytotoxicity

Negative

Immunotoxicity

Positive

 

4. CONCLUSIONS:

The computational analysis of amphemidine is the goal of this study. This congener has more affinity compared to the marketed inhibitors (donepezil, galantamine, rivastigmine) with -9.9 kcal/mol against 1Q5K (GSK-3 antagonist). This Phyto molecule has correctly applied the Lipinski instruction. Additionally, we discovered that the chemical is not harmful from toxicity testing. Consequently, Amphimedine, a natural inhibitor, may have some effect on GSK-3 in silico. The results of this study will aid in developing novel amphimedine congeners that will serve as effective inhibitors of glycogen synthase kinase for the treatment of AD.

 

5. AVAILABILITY OF DATA AND MATERIALS:

The data supporting the findings of the article is available within the article.

 

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GRAPHICAL ABSTRACT:

 

Molecular docking of amphimedine against 1Q5K (GSK-3 inhibitor)

 

 

 

Received on 04.06.2024      Revised on 10.01.2025

Accepted on 14.05.2025      Published on 06.10.2025

Available online from October 13, 2025

Asian J. Pharm. Res. 2025; 15(4):364-368.

DOI: 10.52711/2231-5691.2025.00056

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