scholarly journals Molecular Docking Studies, Bioactivity Score Prediction, Drug Likeness Analysis of GSK-3 β Inhibitors: A Target Protein Involved in Alzheimer’s Disease

2018 ◽  
Vol 15 (2) ◽  
pp. 455-467 ◽  
Author(s):  
Akanksha Joshi ◽  
Rajesh Kumar ◽  
Archit Sharma
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Targets ◽  
Glycogen Synthase ◽  
Acetylcholinesterase Inhibitors ◽  
Docking Studies ◽  
Binding Affinities ◽  
Withanolide A ◽  
Potent Drug ◽  
Reliable Marker

Glycogen synthase kinase 3 β (GSK-3 Beta) is a potential target for developing an effective therapeutic effect in Alzheimer's disease (AD). Currently, no such drug or molecules has been found till date which can cure AD completely. Few drugs such as acetylcholinesterase inhibitors and memantine are ineffective in the later stages of the disease. Therefore, with the advancements in computational biology approaches, it is possible to combat alzheimer’s disease by targeting one of the kinases i.e. GSK-3 β involved in hyper phosphorylation of tau (a reliable marker of neurodegenerative disorders). In this study, we have carried out alzheimer’s structure-based drug designing with GSK-3 β. By applying appropriate docking methodology, we have identified few plant-derived compounds which show enhanced target selectivity than the conventional alzheimer's drug (such as memantine). Here we enumerate the comparison among the current and future AD therapy on the basis of their binding affinities. As a result, a large library of compounds has been screened as potent drug targets. It was also observed that withanolide–A (extracted from roots of withania somnifera) has the potential to emerge as the eventual drug for the AD. Moreover, few other phytocompounds such as celastrol, kenpaullone, quercetin, alsterpaullone have also shown enhanced activity in the decreasing order of their binding affinities.

Molecular drug targets and therapies for Alzheimer’s disease

2014 ◽  
Vol 5 (3) ◽  
Author(s):  
Dev Singh ◽  
Manish Gupta ◽  
Rajesh Kesharwani ◽  
Mamta Sagar ◽  
Seema Dwivedi ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Targets ◽  
Neurodegenerative Disorder ◽  
Glycogen Synthase ◽  
Interaction Analysis ◽  
Memory Loss ◽  
Alpha Synuclein ◽  
Herbal Remedies ◽  
Cholesterol Acyl Transferase

AbstractAlzheimer’s disease (AD) is a neurodegenerative disorder that is characterized by normal memory loss and cognitive impairment in humans. Many drug targets and disease-modulating therapies are available for treatment of AD, but none of these are effective enough in reducing problems associated with recognition and memory. Potential drug targets so far reported for AD are β-secretase, Γ-secretase, amyloid beta (Aβ) and Aβ fibrils, glycogen synthase kinase-3 (GSK-3), acyl-coenzyme A: cholesterol acyl-transferase (ACAT) and acetylcholinesterase (AChE). Herbal remedies (antioxidants) and natural metal-chelators have shown a very significant role in reducing the risk of AD, as well as lowering the effect of Aβ in AD patients. Researchers are working in the direction of antisense and stem cell-based therapies for a cure for AD, which mainly depends on the clearance of misfolded protein deposits — including Aβ, tau, and alpha-synuclein. Computational approaches for inhibitor designing, interaction analysis, principal descriptors and an absorption, distribution, metabolism, excretion and toxicity (ADMET) study could speed up the process of drug development with higher efficacy and less chance of failure. This paper reviews the known drugs, drug targets, and existing and future therapies for the treatment of AD.

scholarly journals Emetine and Indirubin- 3- monoxime interaction with human brain acetylcholinesterase: A computational and statistical analysis

2022 ◽  
Vol 67 (4) ◽  
pp. 106-114
Author(s):  
Syed Sayeed Ahmad ◽  
Haroon Khan ◽  
Mohammad Khalid ◽  
Abdulraheem SA Almalki
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Binding Energy ◽  
Human Brain ◽  
Acetylcholinesterase Inhibitors ◽  
Symptomatic Treatment ◽  
Docking Studies ◽  
Coefficient Of Determination ◽  
Intermolecular Energy ◽  
Brain Acetylcholinesterase

Alzheimer's disease is a chronic neurodegenerative ailment and the most familiar type of dementia in the older population with no effective cure to date. It is characterized by a decrease in memory, associated with the mutilation of cholinergic neurotransmission. Presently, acetylcholinesterase inhibitors have emerged as the most endorsed pharmacological medications for the symptomatic treatment of mild to moderate Alzheimer's disease. This study aimed to research the molecular enzymatic inhibition of human brain acetylcholinesterase by a natural compound emetine and I3M. Molecular docking studies were used to identify superior interaction between enzyme acetylcholinesterase and ligands. Furthermore, the docked acetylcholinesterase-emetine complex was validated statistically using an analysis of variance in all tested conformers. In this interaction, H-bond, hydrophobic interaction, pi-pi, and Cation-pi interactions played a vital function in predicting the accurate conformation of the ligand that binds with the active site of acetylcholinesterase. The conformer with the lowest free energy of binding was further analyzed. The binding energy for acetylcholinesterase complex with emetine and I3M was -9.72kcal/mol and -7.09kcal/mol, respectively. In the current study, the prediction was studied to establish a relationship between binding energy and intermolecular energy (coefficient of determination [R2 linear = 0.999), and intermolecular energy and Van der wall forces (R2 linear = 0.994). These results would be useful in gaining structural insight for designing novel lead compounds against acetylcholinesterase for the effective management of Alzheimer's disease.

Phytochemicals for drug discovery in Alzheimer’s disease: In silico Advances

2020 ◽  
Vol 26 ◽  
Author(s):  
Smriti Sharma ◽  
Vinayak Bhatia
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Design ◽  
In Silico ◽  
Drug Targets ◽  
Development Process ◽  
Phytochemical Analysis ◽  
Computational Drug Design ◽  
Novel Drugs ◽  
Game Changer

: The search for novel drugs that can prevent or control Alzheimer’s disease has attracted lot of attention from researchers across the globe. Phytochemicals are increasingly being used to provide scaffolds to design drugs for AD. In silico techniques, have proven to be a game-changer in this drug design and development process. In this review, the authors have focussed on current advances in the field of in silico medicine, applied to phytochemicals, to discover novel drugs to prevent or cure AD. After giving a brief context of the etiology and available drug targets for AD, authors have discussed the latest advances and techniques in computational drug design of AD from phytochemicals. Some of the prototypical studies in this area are discussed in detail. In silico phytochemical analysis is a tool of choice for researchers all across the globe and helps integrate chemical biology with drug design.

Identifying Alzheimer’s Disease-related miRNA Based on Semi-clustering

2019 ◽  
Vol 19 (4) ◽  
pp. 216-223 ◽  
Author(s):  
Tianyi Zhao ◽  
Donghua Wang ◽  
Yang Hu ◽  
Ningyi Zhang ◽  
Tianyi Zang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Targets ◽  
Molecular Mechanisms ◽  
Feature Vector ◽  
Mirna Gene ◽  
Interaction Network ◽  
Gene Interaction ◽  
Proteinprotein Interaction ◽  
Synaptic Structures

Background: More and more scholars are trying to use it as a specific biomarker for Alzheimer’s Disease (AD) and mild cognitive impairment (MCI). Multiple studies have indicated that miRNAs are associated with poor axonal growth and loss of synaptic structures, both of which are early events in AD. The overall loss of miRNA may be associated with aging, increasing the incidence of AD, and may also be involved in the disease through some specific molecular mechanisms. Objective: Identifying Alzheimer’s disease-related miRNA can help us find new drug targets, early diagnosis. Materials and Methods: We used genes as a bridge to connect AD and miRNAs. Firstly, proteinprotein interaction network is used to find more AD-related genes by known AD-related genes. Then, each miRNA’s correlation with these genes is obtained by miRNA-gene interaction. Finally, each miRNA could get a feature vector representing its correlation with AD. Unlike other studies, we do not generate negative samples randomly with using classification method to identify AD-related miRNAs. Here we use a semi-clustering method ‘one-class SVM’. AD-related miRNAs are considered as outliers and our aim is to identify the miRNAs that are similar to known AD-related miRNAs (outliers). Results and Conclusion: We identified 257 novel AD-related miRNAs and compare our method with SVM which is applied by generating negative samples. The AUC of our method is much higher than SVM and we did case studies to prove that our results are reliable.

Targeting Tau Hyperphosphorylation via Kinase Inhibition: Strategy to Address Alzheimer's Disease

2020 ◽  
Vol 20 (12) ◽  
pp. 1059-1073 ◽  
Author(s):  
Ahmad Abu Turab Naqvi ◽  
Gulam Mustafa Hasan ◽  
Md. Imtaiyaz Hassan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Tau Protein ◽  
Glycogen Synthase ◽  
Paired Helical Filaments ◽  
Tau Hyperphosphorylation ◽  
Microtubule Stabilization ◽  
Extracellular Signal

Microtubule-associated protein tau is involved in the tubulin binding leading to microtubule stabilization in neuronal cells which is essential for stabilization of neuron cytoskeleton. The regulation of tau activity is accommodated by several kinases which phosphorylate tau protein on specific sites. In pathological conditions, abnormal activity of tau kinases such as glycogen synthase kinase-3 β (GSK3β), cyclin-dependent kinase 5 (CDK5), c-Jun N-terminal kinases (JNKs), extracellular signal-regulated kinase 1 and 2 (ERK1/2) and microtubule affinity regulating kinase (MARK) lead to tau hyperphosphorylation. Hyperphosphorylation of tau protein leads to aggregation of tau into paired helical filaments like structures which are major constituents of neurofibrillary tangles, a hallmark of Alzheimer’s disease. In this review, we discuss various tau protein kinases and their association with tau hyperphosphorylation. We also discuss various strategies and the advancements made in the area of Alzheimer's disease drug development by designing effective and specific inhibitors for such kinases using traditional in vitro/in vivo methods and state of the art in silico techniques.

Pharmacophore Modeling and Docking Studies to Investigate Potential Leads for the Development of β -Secretase APP Cleavage Enzyme-1 (BACE-1) Inhibitors

2019 ◽  
Vol 16 (7) ◽  
pp. 775-784
Author(s):  
Richa Arya ◽  
Satya Prakash Gupta ◽  
Sarvesh Paliwal ◽  
Swapnil Sharma ◽  
Kirtika Madan ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Medical Condition ◽  
Pharmacophore Model ◽  
Pharmacophore Modeling ◽  
Docking Studies ◽  
Pyridine Derivative ◽  
Cleavage Enzyme ◽  
Bace 1

Background: Alzheimer’s disease is a medical condition with detrimental brain health. It is majorly diagnosed in aging individuals plaque in β) characterized by accumulated Amyloidal beta (A 1 BACE) 1 secretase APP cleavage enzyme βneurological areas. The ) is the target of choice that can be exploited to find drugs against Alzheimer’s disease. Methods: A series of BACE-1 inhibitors with reported binding constant were considered for the development of a feature based pharmacophore model. Results: The good correlation coefficient (r=0.91) and RMSD of 0.93 was observed with 30 compounds in training set. The model was validated internally (r2test=0.76) as well as externally by Fischer validation. The pharmacophore based virtual screening retrieved compounds that were docked and biologically evaluated. Conclusion: The three structurally diverse molecules were tested by in-vitro method. The pyridine derivative with highest fit value (6.9) exhibited IC50 value of 2.70 µM and thus was found to be the most promising lead molecule as BACE-1 inhibitor.

Spirocyclohexadienones as an Uncommon Scaffold for Acetylcholinesterase Inhibitory Activity

2019 ◽  
Vol 15 (4) ◽  
pp. 373-382 ◽  
Author(s):  
Ralph C. Gomes ◽  
Renata P. Sakata ◽  
Wanda P. Almeida ◽  
Fernando Coelho
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Population Aging ◽  
Acetylcholinesterase Inhibitors ◽  
Acetylcholinesterase Activity ◽  
Docking Study ◽  
Biological Properties ◽  
Ache Inhibitor ◽  
Molecular Docking Study

Background: The most important cause of dementia affecting elderly people is the Alzheimer’s disease (AD). Patients affected by this progressive and neurodegenerative disease have severe memory and cognitive function impairments. Some medicines used for treating this disease in the early stages are based on inhibition of acetylcholinesterase. Population aging should contribute to increase the cases of patients suffering from Alzheimer's disease, thus requiring the development of new therapeutic entities for the treatment of this disease. Methods: The objective of this work is to identify new substances that have spatial structural similarity with donepezil, an efficient commercial drug used for the treatment of Alzheimer's disease, and to evaluate the capacity of inhibition of these new substances against the enzyme acetylcholinesterase. Results: Based on a previous results of our group, we prepared a set of 11 spirocyclohexadienones with different substitutions patterns in three steps and overall yield of up to 59%. These compounds were evaluated in vitro against acetylcholinesterase. We found that eight of them are able to inhibit the acetylcholinesterase activity, with IC50 values ranging from 0.12 to 12.67 µM. Molecular docking study indicated that the spirocyclohexadienone, 9e (IC50 = 0.12 µM), a mixedtype AChE inhibitor, showed a good interaction at active site of the enzyme, including the cationic (CAS) and the peripheral site (PAS). Conclusion: We described the first study aimed at investigating the biological properties of spirocyclohexadienones as acetylcholinesterase inhibitors. Thus, we have identified an inhibitor, which provided valuable insights for further studies aimed at the discovery of more potent acetylcholinesterase inhibitors.

Systematic Design and Evaluation of Drug Repurposing-Oriented Alzheimer’s Disease Ontology (Preprint)

2020 ◽  
Author(s):  
Fang Li ◽  
Muhammad "Tuan" Amith ◽  
Grace Xiong ◽  
Jingcheng Du ◽  
Yang Xiang ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Drug Targets ◽  
Drug Repurposing ◽  
Essential Elements ◽  
Genomic Research ◽  
Core Knowledge ◽  
Disease Ontology ◽  
Hybrid Strategy ◽  
Complementary Strategy

BACKGROUND Alzheimer’s Disease (AD) is a devastating neurodegenerative disease, of which the pathophysiology is insufficiently understood, and the curative drugs are long-awaited to be developed. Computational drug repurposing introduces a promising complementary strategy of drug discovery, which benefits from an accelerated development process and decreased failure rate. However, generating new hypotheses in AD drug repurposing requires multi-dimensional and multi-disciplinary data integration and connection, posing a great challenge in the era of big data. By integrating data with computable semantics, ontologies could infer unknown relationships through automated reasoning and fulfill an essential role in supporting computational drug repurposing. OBJECTIVE The study aimed to systematically design a robust Drug Repurposing-Oriented Alzheimer’s Disease Ontology (DROADO), which could model fundamental elements and their relationships involved in AD drug repurposing and integrate their up-to-date research advance comprehensively. METHODS We devised a core knowledge model of computational AD drug repurposing, based on both pre-genomic and post-genomic research paradigms. The model centered on the possible AD pathophysiology and abstracted the essential elements and their relationships. We adopted a hybrid strategy to populate the ontology (classes and properties), including importing from well-curated databases, extracting from high-quality papers and reusing the existing ontologies. We also leveraged n-ary relations and nanopublication graphs to enrich the object relations, making the knowledge stored in the ontology more powerful in supporting computational processing. The initially built ontology was evaluated by a semiotic-driven and web-based tool Ontokeeper. RESULTS The current version of DROADO was composed of 1,021 classes, 23 object properties and 3,207 axioms, depicting a fundamental network related to computational neuroscience concepts and relationships. Assessment using semiotic evaluation metrics by OntoKeeper indicated sufficient preliminary quality (semantics, usefulness and community-consensus) of the ontology. CONCLUSIONS As an in-depth knowledge base, DROADO would be promising in enabling computational algorithms to realize supervised mining from multi-source data, and ultimately, facilitating the discovery of novel AD drug targets and the realization of AD drug repurposing.

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