Design of novel amyloid β aggregation inhibitors using QSAR, pharmacophore modeling, molecular docking and ADME prediction
Lilly Aswathy,Radhakrishnan S. Jisha,Vijay H. Masand,Jayant M. Gajbhiye,Indira G. Shibi +4 more
- Vol. 6, Iss: 1, pp 12-12
TLDR
2D-QSAR, HQSAR and 3D QSAR models are adopted to identify the structural and physicochemical requirements for the potential Aβ aggregation inhibition and provide explanation of the important features, like steric, electrostatic and hydrogen bond acceptor, which play important role for interaction with the receptor site cavity.Abstract:
The inhibition of abnormal amyloid β (Aβ) aggregation has been regarded as a good target to control Alzheimer’s disease. The present study adopted 2D-QSAR, HQSAR and 3D QSAR (CoMFA & CoMSIA) modeling approaches to identify the structural and physicochemical requirements for the potential Aβ aggregation inhibition. A structure-based molecular docking technique is utilized to approve the features that are obtained from the ligand-based techniques on 30 curcumin derivatives. The combined outputs were then used to screen the modified 10 compounds. The 2D QSAR model on curcumin derivatives gave statistical values R2 = 0.9086 and SEE = 0.1837. The model was further confirmed by Y-randomization test and Applicability domain analysis by the standardization approach. The HQSAR study (Q2 = 0.615, R
ncv
2
= 0.931, R
pred
2
= 0.956) illustrated the important molecular fingerprints for inhibition. Contour maps of 3D QSAR models, CoMFA (Q2 = 0.687, R
ncv
2
= 0.787, R
pred
2
= 0.731) and CoMSIA (Q2 = 0.743, R
ncv
2
= 0.972, R
pred
2
= 0.713), depict that the models are robust and provide explanation of the important features, like steric, electrostatic and hydrogen bond acceptor, which play important role for interaction with the receptor site cavity. The molecular docking study of the curcumin derivatives elucidates the important interactions between the amino acid residues at the catalytic site of the receptor and the ligands, indicating the structural requirements of the inhibitors. The ligand–receptor interactions of top hits were analyzed to explore the pharmacophore features of Aβ aggregation inhibition. The Aβ aggregation inhibitory activities of novel chemical entities were then obtained through inverse QSAR. The newly designed molecules were further screened through machine learning, prediction of toxicity and nature of metabolism to get the proposed six lead compounds.read more
Citations
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Computational Approaches in Preclinical Studies on Drug Discovery and Development.
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TL;DR: A systematic classification and description of the databases and software commonly used for ADMET prediction and some applications that are related to the prediction categories and web tools are listed.
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Curcumin in Health and Diseases: Alzheimer's Disease and Curcumin Analogues, Derivatives, and Hybrids.
TL;DR: A review of bibliographical data from 2009 to 2019 on curcumin analogues, derivatives, and hybrids, as well as their therapeutic, preventic, and diagnostic applications in AD, reveals that the phenolic hydroxyl group could contribute to the anti-amyloidogenic activity.
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Diana Larisa Roman,Marin Roman,Claudia Som,Mélanie Schmutz,Edgar Hernandez,Peter Wick,Tommaso Casalini,Giuseppe Perale,Vasile Ostafe,Adriana Isvoran +9 more
TL;DR: The computational assessment showed that investigated chito-oligomers reflect promising pharmacological profiles and limited toxicological effects on humans, regardless of molecular weight, deacetylation degree, and acetylation pattern.
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On the Conformational Dynamics of β-Amyloid Forming Peptides: A Computational Perspective
TL;DR: This article comprehensively reviewed the developmental advances in the theoretical models for Aβ peptide folding and interactions, particularly in the context of neurological disorders, and extensively reviewed the advances in molecular dynamics simulation as a tool used for studying the conversions between polymorphic amyloid forms and applications of using machine learning approaches in predicting A β peptides and aggregation-prone regions in proteins.
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