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Showing 2 results for Molecular Docking
The Suggestion of a Drug for COVID-19 with Molecular Docking
Reihaneh Sabbaghzadeh,
Volume 17, Issue 2 (3-2023)
Abstract
Background and objectives: This study aimed to study the interaction between the severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) spike protein complex and seven drugs that inhibit the angiotensin-converting enzyme 2.
Methods: Plots of protein-ligand interaction were obtained using the LigPlot software. In addition, binding energies in kcal/mol, hydrophobic interactions, and hydrogen bonds were determined. Autodock software v.1.5.6 and AutoDock Vina were used for the analysis of molecular docking processes.
Results: The only structure that interacted with the SARS‑CoV‑2 spike protein was anakinra.
Conclusion: Anakinra was the only drug that interacted with the SARS‑CoV‑2 spike protein. This could be further investigated for finding a temporary alternative medicine for the treatment of coronavirus disease 2019.
Investigating the role of miR-30c in modulating γ-secretase activity: Implications for Alzheimer’s disease
Taiebeh Kafshdooz Pourpolsangi, Rasoul Sharifi , Safar Farajnia , Safa Najmi ,
Volume 19, Issue 6 (11-2025)
Abstract
Background: Alzheimer’s disease (AD), the most common form of dementia, affects millions of people worldwide. Clinical trials using anti-Aβ antibodies demonstrate that amyloid plaque removal in early-stage AD can slow disease progression. Along with β-secretase, γ-secretase plays a role in cleaving amyloid precursor protein (APP). The aim of this study was to use computational docking to identify molecules that can activate γ-secretase.
Methods: Initially, the targets of hsa-miR-30c-5p were assessed using the TargetScanHuman server. The structure of γ-secretase was prepared in Chimera by removing non-standard residues and water molecules. Adjacent amino acids to the cholesterol ligand were then identified using PyMOL. The 3D structure and SMILES notation for cholesterol were obtained from PubChem. Docking results in pdbqt format were analyzed using Discovery Studio, LigPlus+, and PDBsum, with LigPlus+ focusing on protein subunit interactions.
Results: The TargetScanHuman server indicated that γ-secretase is a target of hsa-miR-30c-5p. Drug-like properties (Solubility, tumorigenicity, LogP, toxicity) of compounds were predicted using tools such as SwissTargetPrediction, PASS-Way2Drug, and SwissADME, following Lipinski’s Rule of Five. Amino acids Trp227, Leu192, Arg186, Leu199, Leu203, Leu206, Tyr155, Leu215, Phe162, Ser223, and Ile230, located on the γ-secretase C subunit, were analyzed for interactions using LigPlot after AutoDock Vina docking and Chimera visualization.
Conclusion: These in silico findings suggest cholesterin acetate as a potential activator of γ-secretase; further experimental validation is warranted.
 

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