Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics

Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics

Bibliographic Details
Main Author: Ghiasi, Zahra
Language:English
Published: Ohio University / OhioLINK 2021
Subjects:
Biomedical Engineering
Bioinformatics
Chemical Engineering
GSK-3 protein
computational drug discovery
ligand docking
RDKit
Rosetta
AutoDock Vina
Online Access:http://rave.ohiolink.edu/etdc/view?acc_num=ohiou162861276157897
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spelling ndltd-OhioLink-oai-etd.ohiolink.edu-ohiou1628612761578972021-09-11T05:17:14Z Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics Ghiasi, Zahra Biomedical Engineering Bioinformatics Chemical Engineering GSK-3 protein computational drug discovery ligand docking RDKit Rosetta AutoDock Vina Glycogen synthase kinase 3 (GSK-3) has been validated as a critical therapeutic target inmany inflammatory diseases. This project is focused on developing a computationalmechanism to design new drug-like molecules and screen for those molecules that canstrongly bind to GSK-3. We developed a computational methodology to generate apopulation of small molecules starting from some seed molecules and identifying theones that have chemical properties similar to those observed in drug molecules. In thenext step, we performed a protein-ligand docking using ROSETTA and AutoDock Vina toidentify the ligands that can strongly bind to GSK-3. This research demonstrates thatROSETTA and AutoDock Vina are not accurate enough to distinguish between moleculesthat are similar in size and share many molecular fragments. Docking methods are usefulfor determining a chemical space where strong binders are likely to be found. ROSETTAshowed that small molecules with molecular weight close to 342 Da are of optimum sizeto strongly bind to GSK-3 binding pocket. 2021-09-10 English text Ohio University / OhioLINK http://rave.ohiolink.edu/etdc/view?acc_num=ohiou162861276157897 http://rave.ohiolink.edu/etdc/view?acc_num=ohiou162861276157897 restricted--full text unavailable until 2022-09-01 This thesis or dissertation is protected by copyright: all rights reserved. It may not be copied or redistributed beyond the terms of applicable copyright laws.
collection NDLTD
language English
sources NDLTD
topic Biomedical Engineering
Bioinformatics
Chemical Engineering
GSK-3 protein
computational drug discovery
ligand docking
RDKit
Rosetta
AutoDock Vina
spellingShingle Biomedical Engineering
Bioinformatics
Chemical Engineering
GSK-3 protein
computational drug discovery
ligand docking
RDKit
Rosetta
AutoDock Vina
Ghiasi, Zahra
Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
author Ghiasi, Zahra
author_facet Ghiasi, Zahra
author_sort Ghiasi, Zahra
title Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
title_short Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
title_full Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
title_fullStr Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
title_full_unstemmed Development of a Computational Mechanism to Generate Molecules with Drug-likeCharacteristics
title_sort development of a computational mechanism to generate molecules with drug-likecharacteristics
publisher Ohio University / OhioLINK
publishDate 2021
url http://rave.ohiolink.edu/etdc/view?acc_num=ohiou162861276157897
work_keys_str_mv AT ghiasizahra developmentofacomputationalmechanismtogeneratemoleculeswithdruglikecharacteristics
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