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Dissertations / Theses on the topic 'Ligand based drug design'

Author: Grafiati

Published: 12 August 2021

Last updated: 25 July 2025

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1

Nilapwar, S. "Characterization and exploitation of protein ligand interactions for structure based drug design." Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/19034/.

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Most characterised protein-small molecule interactions that display a change in heat capacity (\bigtriangleupCp) occur with a negative \bigtriangleupCp value. This is often attributed to solvent reorganisation from reduction in solvent accessible apolar surface area accompanying complex formation. Positive \bigtriangleupCp values have not been widely reported and could typically be attributed to an increased solvent accessible apolar surface area, desolvation of polar surface area or structural transitions in the biomolecular complex. Heat shock protein-90 (Hsp90) is one of the abundant and im

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2

Li, Huameng. "Multiple Ligand Simultaneous Docking (MLSD) and Its Applications to Fragment Based Drug Design and Drug Repositioning." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1324606149.

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3

Davis, Caroline M. "Investigation and Characterisation of Protein-Ligand Interactions: SRA-Ribonucleic Acid Recognition and Anti-Microbial Drug Discovery." University of Akron / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=akron1437779075.

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4

Kumari, Vandana. "Structure-Based Computer Aided Drug Design and Analysis for Different Disease Targets." The Ohio State University, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=osu1311612599.

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5

Mukherjee, Prasenjit. "Use of molecular modeling tools in the elucidation of ligand-macromolecular interactions and applications in structure-based drug design /." Full text available from ProQuest UM Digital Dissertations, 2008. http://0-proquest.umi.com.umiss.lib.olemiss.edu/pqdweb?index=0&did=1850501401&SrchMode=1&sid=4&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1277323802&clientId=22256.

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Thesis (Ph.D.)--University of Mississippi, 2008.<br>Typescript. Vita. Major professor: Mitchell A. Avery Includes bibliographical references (leaves 246-259). Also available online via ProQuest to authorized users.

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6

Park, In-Hee. "Computational Simulations of Protein-Ligand Molecular Recognition via Enhanced Samplings, Free Energy Calculations and Applications to Structure-Based Drug Design." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1276745410.

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7

Zephyr, Jacqueto. "Robust Drug Design Strategies and Discovery Targeting Viral Proteases." eScholarship@UMMS, 2021. https://escholarship.umassmed.edu/gsbs_diss/1157.

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Viral proteases play crucial roles in the life cycle and maturation of many viruses by processing the viral polyprotein after translation and in some cases cleaving host proteins associated with the immune response. The essential role of viral proteases makes them attractive therapeutic targets. In this thesis, I provide an introductory summary of viral proteases, their structure, mechanism, and inhibition, while the breadth of this thesis focuses on the Hepatitis C virus (HCV) NS3/4A and Zika virus (ZIKV) NS2B/NS3 viral proteases. HCV NS3/4A protease inhibitors (PIs) have become a mainstay in

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8

Dean, Sondra Faye. "Ligand-associated conformational changes of a flexible enzyme captured by harnessing the power of allostery." Thesis, University of Iowa, 2016. https://ir.uiowa.edu/etd/2201.

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Flexible enzymes are notoriously a bane to structure-based drug design and discovery efforts. This is because no single structure can accurately capture the vast array of conformations that exist in solution and many are subject to ligand-associated structural changes that are difficult to predict. Glutamate racemase (GR) – an antibiotic drug discovery target involved in cell wall biosynthesis – is one such enzyme that has eluded basic structure-based drug design and discovery efforts due to these flexibility issues. In this study, our focus is on overcoming the impediment of unpredictable lig

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9

Barelier, Sarah. "Probing protein-small molecule interactions by Nuclear Magnetic Resonance : towards a better understanding of the Fragment-Based Drug Design methodology." Thesis, Lyon 1, 2010. http://www.theses.fr/2010LYO10222.

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La méthode de conception de médicaments à partir de molécules « fragments » (connue sous le nom de « Fragment-Based Drug Design ») a été proposée au milieu des années 90, et a depuis été reconnue comme une alternative tangible aux techniques plus classiques de recherche de médicaments telles que le criblage à haut débit par exemple. La méthode des fragments consiste à cribler un petit nombre (< 10000) de composés organiques de faible poids moléculaire (< 300 Da) afin de détecter ceux qui se lient à la cible (protéine ou acides nucléiques). Du fait de leur faible complexité, les fragments

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10

AIROLDI, CRISTINA. "Development of new potential antitumor drugs based on Ras protein inhibition." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2007. http://hdl.handle.net/10281/116562.

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Because of their role in oncogenesis, inhibition of Ras proteins, particularly of their tumorigenic variants, represents today one of the principal strategies finalized to the obtainment of new antitumoral therapies. Among the different possible approaches, one of the most innovative and less explored is represented by the inhibition of this protein activation, key event for the explication of their biological activity, but also for the Ras-induced tumoral cell transformation. Objective of this thesis has been the development of new small molecules able to inhibit, at least partially (total i

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11

Morizzo, Erika. "G Protein-Coupled Receptors as Potential Drug Target: From Receptor Topology to Rational Drug Design, an in-silico Approach." Doctoral thesis, Università degli studi di Padova, 2009. http://hdl.handle.net/11577/3426081.

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G protein-coupled receptors (GPCRs) constitute a very large family of heptahelical, integral membrane proteins that mediate a wide variety of physiological processes, ranging from the transmission of the light and odorant signals to the mediation of neurotransmission and hormonal actions. GPCRs are dysfunctional or deregulated in several human diseases and are estimated to be the target of more than 40% of drugs used in clinical medicine today. The crystal structures of rhodopsin and the recent published crystal structures of beta-adrenergic receptors and human A2A Adrenergic Receptor pr

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12

Tai, Hio Kuan. "Protein-ligand docking and virtual screening based on chaos-embedded particle swarm optimization algorithm." Thesis, University of Macau, 2018. http://umaclib3.umac.mo/record=b3948431.

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13

Berry, Michael. "Massively-Parallel Computational Identification of Novel Broad Spectrum Antivirals to Combat Coronavirus Infection." University of the Western Cape, 2015. http://hdl.handle.net/11394/8321.

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Philosophiae Doctor - PhD<br>Given the significant disease burden caused by human coronaviruses, the discovery of an effective antiviral strategy is paramount, however there is still no effective therapy to combat infection. This thesis details the in silica exploration of ligand libraries to identify candidate lead compounds that, based on multiple criteria, have a high probability of inhibiting the 3 chymotrypsin-like protease (3CUro) of human coronaviruses. Atomistic models of the 3CUro were obtained from the Protein Data Bank or theoretical models were successfully generated by homology m

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14

Berg, Lotta. "Exploring non-covalent interactions between drug-like molecules and the protein acetylcholinesterase." Doctoral thesis, Umeå universitet, Kemiska institutionen, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-129900.

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The majority of drugs are small organic molecules, so-called ligands, that influence biochemical processes by interacting with proteins. The understanding of how and why they interact and form complexes is therefore a key component for elucidating the mechanism of action of drugs. The research presented in this thesis is based on studies of acetylcholinesterase (AChE). AChE is an essential enzyme with the important function of terminating neurotransmission at cholinergic synapses. AChE is also the target of a range of biologically active molecules including drugs, pesticides, and poisons. Due

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15

LA, MONICA Gabriele. "Correlation between cell line chemosensitivity and protein expression pattern as new approach for the design of targeted anticancer small molecules." Doctoral thesis, Università degli Studi di Palermo, 2022. https://hdl.handle.net/10447/573085.

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BACKGROUND AND RATIONALE: Over the past few decades, several databases with a significant amount of biological data related to cancer cells and anticancer agents (e.g.: National Cancer Institute database, NCI; Cancer Cell Line Encyclopedia, CCLE; Genomic and Drug Sensitivity in Cancer portal, GDSC) have been developed. The huge amount of heterogeneous biological data extractable from these databanks (among all, drug response and protein expression) provides a real foundation for predictive cancer chemogenomics, which aims to investigate the relationships between genomic traits and the response

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16

AbdulHameed, Mohamed Diwan Mohideen. "COMPUTATIONAL DESIGN OF 3-PHOSPHOINOSITIDE DEPENDENT KINASE-1 INHIBITORS AS POTENTIAL ANTI-CANCER AGENTS." UKnowledge, 2009. http://uknowledge.uky.edu/gradschool_diss/757.

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Computational drug design methods have great potential in drug discovery particularly in lead identification and lead optimization. 3-Phosphoinositide dependent kinase-1 (PDK1) is a protein kinase and a well validated anti-cancer target. Inhibitors of PDK1 have the potential to be developed as anti-cancer drugs. In this work, we have applied various novel computational drug design strategies to design and identify new PDK1 inhibitors with potential anti-cancer activity. We have pursued novel structure-based drug design strategies and identified a new binding mode for celecoxib and its derivati

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17

Yang, Hui. "Theoretical Studies of Molecular Recognition in Protein-Ligand and Protein-Protein Complexes." University of Toledo / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=toledo1282339026.

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18

McConnell, Brendan Neil. "Fragment-based approaches to targeting EthR from mycobacterium tuberculosis." Thesis, University of Cambridge, 2019. https://www.repository.cam.ac.uk/handle/1810/290255.

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Tuberculosis affects millions of people worldwide every year. The current treatment for TB is divided into a regimen of both first- and second-line drugs, where first-line treatments are more tolerated and require shorter treatment lengths. With rising levels of resistance, alternative treatment regimes are urgently needed to fight this disease. Ethionamide, a second-line drug is administered as a prodrug which is activated in vivo by the enzyme EthA, which is in turn regulated by EthR. The disruption of the action of EthR could lead to novel therapeutics which could enhance the efficacy of et

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19

Khattri, Ram Bahadur. "Identifying selective ligands for glutaredoxin proteins with fragment based drug design approach and optimization of the bacterial selective hits." University of Akron / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=akron1460988438.

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20

González-Alemán, Roy. "Computational fragment-based design of chemically modified oligonucleotides for selective protein inhibition : BACE1 as a case study." Electronic Thesis or Diss., université Paris-Saclay, 2023. http://www.theses.fr/2023UPASL149.

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La conception de médicaments à base de fragments (FBDD) est devenue une approche de plus en plus populaire dans la conception de ligand, avec de nombreuses réussites dans le processus de découverte de médicaments. Malgré certains défis liés à l'accessibilité synthétique et aux stratégies de conception de ligand, le FBDD reste une méthode prometteuse pour aborder l'espace chimique, la complexité moléculaire, la probabilité de liaison et l'efficacité des ligands. Les thérapies à ARN se développent rapidement, subissant une résurgence en raison des nombreux avantages de ces molécules par rapport

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21

Folly, da Silva Constantino Laura. "An effective layered workflow of virtual screening for identification of active ligands of challenging protein targets." Thesis, University of Iowa, 2017. https://ir.uiowa.edu/etd/5754.

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Docking is a computer simulation method used to predict the preferred orientation of two interacting chemical species that has been successfully applied to numerous macromolecules over the years. However, non-traditional targets have inherent difficulties associated with their screening. Large interfaces, lack of obvious binding sites, and transient pockets are some examples. Additionally, most natural ligands of challenging targets are inadequate models for identifying or designing new ligands. Therefore, it is not surprising that customary techniques of structure-based virtual screening are

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22

Panei, Francesco Paolo. "Advanced computational techniques to aid the rational design of small molecules targeting RNA." Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS106.

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Les molécules d'ARN sont devenues des cibles thérapeutiques majeures, et le ciblage par petites molécules se révèle particulièrement prometteur. Cependant, malgré leur potentiel, le domaine est encore en développement, avec un nombre limité de médicaments spécifiquement conçus pour l'ARN. La flexibilité intrinsèque de l'ARN, bien qu'elle constitue un obstacle, introduit des opportunités thérapeutiques que les outils computationnels actuels ne parviennent pas pleinement à exploiter malgré leur prédisposition. Le projet de cette thèse est de construire un cadre computationnel plus complet pour l

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23

Chiesa, Luca. "Development of artificial intelligence methods to help the design of new ligands of G-protein coupled receptors." Electronic Thesis or Diss., Strasbourg, 2024. http://www.theses.fr/2024STRAF020.

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Les récepteurs couplés aux protéines G représentent l'une des familles de protéines les plus importantes pour la découverte de médicaments. Les techniques de conception de médicaments assistée par ordinateur ont été largement appliquées pour cibler les membres de cette famille, conduisant à la découverte de multiples molécules bioactives. Cette thèse décrit le développement, le test et l'application de différents outils informatiques et d'apprentissage automatique pour aider à la découverte de nouveaux composés présentant un profil pharmacologique souhaité. Divers aspects du processus de décou

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24

Doudou, Slimane. "Computational modelling of protein-ligand binding : steps towards better drug design." Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.498949.

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25

Boas, F. Edward. "Physics-based design of protein-ligand binding /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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26

Davies, Thomas Glanmor. "Protein-ligand interactions for the OppA system." Thesis, University of York, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.311012.

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27

Alvarsson, Jonathan. "Ligand-based Methods for Data Management and Modelling." Doctoral thesis, Uppsala universitet, Institutionen för farmaceutisk biovetenskap, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-248964.

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Drug discovery is a complicated and expensive process in the billion dollar range. One way of making the drug development process more efficient is better information handling, modelling and visualisation. The majority of todays drugs are small molecules, which interact with drug targets to cause an effect. Since the 1980s large amounts of compounds have been systematically tested by robots in so called high-throughput screening. Ligand-based drug discovery is based on modelling drug molecules. In the field known as Quantitative Structure–Activity Relationship (QSAR) molecules are described by

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28

Toschi, Francesca. "The computational investigation of protein/ligand complexes : implications for rational drug design." Thesis, University of Southampton, 2004. https://eprints.soton.ac.uk/378844/.

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29

Calabrò, Gaetano. "Accelerating molecular simulations : implication for rational drug design." Thesis, University of Edinburgh, 2015. http://hdl.handle.net/1842/16439.

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The development and approval of new drugs is an expensive process. The total cost for the approval of a new compound is on average 1.0 - 1.2 billion dollars and the entire process lasts about 12 - 15 years. The main difficulties are related to poor pharmacokinetics, lack of efficacy and unwanted side effects. These problems have naturally led to the question if new and alternative methodologies can be developed to find reliable and low cost alternatives to existing practices. Nowadays, computer-assisted tools are used to support the decision process along the early stages of the drug discovery

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30

Venot, Pierre-Etienne. "Synthèse stéréosélective d'Hybrides de lobéline et de ligands naturels des récepteurs nicotiniques centraux à l’acétylcholine." Thesis, Paris 11, 2015. http://www.theses.fr/2015PA114813/document.

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Au cours de ce travail, nous avons développé des voies de synthèses convergentes et énantiosélectives en vue de préparer des analogues pyrrolidiniques des alcaloïdes de Lobelia comme nouveaux ligands des récepteurs nicotiniques à l’acétylcholine. Deux familles de ligands ont été réalisées par des méthodes d’élongation mono- ou bi-directionnelle basées respectivement sur des stratégies de désymétrisation précoce ou tardive au départ du succinaldéhyde.La première partie de ce manuscrit aborde la conception d’hybrides de lobéline, nicotine et d’agonistes naturels. Ces structures originales ont ét

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31

Mazzolari, A. "IN SILICO APPROACHES IN DRUG DESIGN AND DEVELOPMENT: APPLICATIONS TO RATIONAL LIGAND DESIGN AND METABOLISM PREDICTION." Doctoral thesis, Università degli Studi di Milano, 2015. http://hdl.handle.net/2434/347523.

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In the last decades, the applications of computational methods in medicinal chemistry have experienced significant changes which have incredibly expanded their approaches, and more importantly their objectives. The overall aim of the present research project is to explore the different fields of the modelling studies by using well-known computational methods as well as different and innovative techniques. Indeed, computational methods traditionally consisted in ligand-based and the structure-based approaches substantially aimed at optimizing the ligand structure in terms of affinity, potenc

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32

Arvidsson, Staffan. "Automating model building in ligand-based predictive drug discovery using the Spark framework." Thesis, Uppsala universitet, Institutionen för biologisk grundutbildning, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-255610.

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Automation of model building enables new predictive models to be generated in a faster, easier and more straightforward way once new data is available to predict on. Automation can also reduce the demand for tedious bookkeeping that is generally needed in manual workflows (e.g. intermediate files needed to be passed between steps in a workflow). The applicability of the Spark framework related to the creation of pipelines for predictive drug discovery was here evaluated and resulted in the implementation of two pipelines that serves as a proof of concept. Spark is considered to provide good me

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33

Hevener, Kirk Edward. "Structure- and ligand-based design of novel antimicrobial agents." View the abstract Download the full-text PDF version, 2008. http://etd.utmem.edu/ABSTRACTS/2008-052-Hevener-index.htm.

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Thesis (Ph.D.)--University of Tennessee Health Science Center, 2008.<br>Title from title page screen (viewed on February 2, 2009). Research advisor: Richard E. Lee, Ph.D. Document formatted into pages (xviii, 238 p. : ill.). Vita. Abstract. Includes bibliographical references (p. 167-186).

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34

Yagnik, Asutosh Trilochan. "Molecular modelling applications in rational drug design and the study of enzyme-ligand interactions." Thesis, University of Exeter, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.245931.

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35

Kekenes-Huskey, Peter Michael Heath James R. Goddard William A. "A Monte Carlo-based torsion construction algorithm for ligand design /." Diss., Pasadena, Calif. : California Institute of Technology, 2009. http://resolver.caltech.edu/CaltechETD:etd-05282009-131419.

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36

Mukherjee, Sreya. "Applications of Molecular Modelling and Structure Based Drug Design in Drug Discovery." Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6331.

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Calcium ions have important roles in cellular processes including intracellular signaling, protein folding, enzyme activation and initiation of programmed cell death. Cells maintain low levels of calcium in their cytosol in order to regulate these processes. When activation of calcium-dependent processes is needed, cells can release calcium stored in the endoplasmic reticulum (ER) into the cytosol to initiate the processes. This can also initiate formation of plasma membrane channels that allow entry of additional calcium from the extracellular milieu. The change in calcium levels is referred

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37

Ward, Richard. "Targeting inositol monophosphatase in structure-based drug design." Thesis, University of Birmingham, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.289291.

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38

Jaiyong, Panichakorn. "Computational modelling of ligand shape and interactions for medicines design." Thesis, University of Manchester, 2016. https://www.research.manchester.ac.uk/portal/en/theses/computational-modelling-of-ligand-shape-and-interactions-for-medicines-design(28d49921-447f-4ea1-aaf2-aa764f45b2f2).html.

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Computational methods have been extensively developed at various levels of approximation in recent years to model biomolecular interactions and for rational drug design. This research work aims to explore the feasibility of using quantum mechanical (QM) methods within the two broad categories of in silico ligand-based and structure-based drug design. First, density functional theory at the M06L level of theory was employed to examine structure-activity relationships of boron-based heterocyclic compounds, anti-inflammatory inhibitors targetting the interleukin-1β (IL-1β) cytokine. Our findings

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CHHABRA, MONICA. "Modeling and Analysis of Ligand Docking to Norovirus Capsid Protein for the Computer-Aided Drug Design." University of Cincinnati / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1209001634.

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Khashan, Raed Saeed Tropsha Alexander. "Development and application of ligand-based and structure-based computational drug discovery tools based on frequent subgraph mining of chemical structures." Chapel Hill, N.C. : University of North Carolina at Chapel Hill, 2007. http://dc.lib.unc.edu/u?/etd,1243.

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Thesis (Ph. D.)--University of North Carolina at Chapel Hill, 2007.<br>Title from electronic title page (viewed Mar. 26, 2008). " ... in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the School of Pharmacy (Division of Medicinal Chemistry and Natural Products)." Discipline: Medicinal Chemistry and Natural Products; Department/School: Pharmacy.

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Salmaso, Veronica. "Exploring protein flexibility during docking to investigate ligand-target recognition." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3421817.

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Ligand-protein binding models have experienced an evolution during time: from the lock-key model to induced-fit and conformational selection, the role of protein flexibility has become more and more relevant. Understanding binding mechanism is of great importance in drug-discovery, because it could help to rationalize the activity of known binders and to optimize them. The application of computational techniques to drug-discovery has been reported since the 1980s, with the advent computer-aided drug design. During the years several techniques have been developed to address the protein flexibil

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Thorsteinson, Nels. "Computational ligand discovery for the human and zebrafish sex hormone binding globulin." Thesis, University of British Columbia, 2008. http://hdl.handle.net/2429/943.

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Virtual screening is a fast, low cost method to identify potential small molecule therapeutics from large chemical databases for the vast amount of target proteins emerging from the life sciences and bioinformatics. In this work, we applied several conventional and newly developed virtual screening approaches to identify novel non-steroidal ligands for the human and zebrafish sex hormone binding globulin (SHBG). The ‘benchmark set of steroids’ is a set of steroids with known affinities for human SHBG that has been widely used for validation in the development of different virtual screening met

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Chemi, Giulia. "Computer-aided drug discovery methodologies for the identification and optimization of bioactive compounds." Doctoral thesis, Università di Siena, 2020. http://hdl.handle.net/11365/1095491.

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In silico methodologies have become an essential part of the modern drug discovery process. This thesis covers a wide range of computational approaches, and all the techniques employed can be grouped and divided in two big different classes: Ligand-Based methods and Structure-Based methods. Particular attention was payed to the evaluation of drug-like features of the identified molecules during both Structure-Based and Ligand-Based projects, in order to propose hit compounds with satisfactory pharmacokinetic profiles. This thesis work is divided in two main chapters according to the two met

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Schmidtke, Peter. "Protein-ligand binding sites. Identification, characterization and interrelations." Doctoral thesis, Universitat de Barcelona, 2011. http://hdl.handle.net/10803/51340.

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El trabajo presentado en esta tesis cubre varios campos de investigación relacionados con el desarrollo de moléculas bioactivas. Se compone de cinco partes distintas que se resumen aquí. Predicción de la utilidad farmacológica de dianas terapéuticas. El desarrollo de fármacos está generalmente dirigido a inhibir la función de una proteína específica. Pero para validar esta proteína como diana terapéutica, al principio de un proyecto de descubrimiento de fármacos se tiene que saber si una molécula de tipo fármaco puede unirse con suficiente afinidad a la proteína como para alterar su func

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Haldoupis, Ioannis. "The application of physics-based rescoring in drug design." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/380891/.

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Most drugs exert their action by binding to a macromolecule target, e.g. a protein. Hence estimating the binding affinity, using computer programs, is of utmost importance in the drug design process. Approximate free energy methods such as MM-PBSA/GBSA appear as attractive alternatives to rigorous free energy methodology. Recently, simplified versions of MM-PBSA/GBSA have been shown to give encouraging results for use as a fast rescoring tool of docked poses in the lead optimisation stage. The primary aim of this work is to ascertain the capability of the method in this context. First the repr

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Nomkoko, Thembelani Edmund. "Computer-aided chemical speciation in metal-based drug design." Doctoral thesis, University of Cape Town, 2002. http://hdl.handle.net/11427/21347.

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Formation constants of Cu²⁺, Ni²⁺, Zn²⁺, Ca²⁺ and Gd³⁺ with the polyamine(amide) ligands N,N' -bis(2-hydroxyiminopropionyl) propane-1,3-diamine (L² ) and (1, 15)- bis(N,N-dimethyl)-5, 11-dioxo-8-(N-benzyl)-l ,4,8, 12, 15-pentaazapentadecane (L³ ) as well as those of Gd³⁺ with 3,3,9,9-tetramethyl-4,8-diazaundecane-2,10-dione dioxime (L 1 ) were investigated by glass electrode potentiometry at 25°C and an ionic strength (I) of 0.15 mol dm-³.

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47

Schulz, Michèle Nadine. "Fragment based ligand discovery : library design and screening by thermal shift analysis." Thesis, University of York, 2012. http://etheses.whiterose.ac.uk/3133/.

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Abstract:

The central idea in Fragment Based Ligand Discovery (FBLD) is to identify small, low molecular weight compounds (MW < 250) that bind to a particular protein active site. Hits can be used to efficiently design larger compounds with the desired affinity and selectivity. Three approaches to FBLD are described in this thesis. The first topic is the development and assessment of different chemoinformatics procedures to select those fragments that maximally represent the chemical features of a larger compound library. Such a fragment library could be of great value in the so-called “SAR by Catalogue

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48

Wang, Feng. "Structure-based drug mechanism study and inhibitor design targeting tuberculosis." [College Station, Tex. : Texas A&M University, 2007. http://hdl.handle.net/1969.1/ETD-TAMU-1439.

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49

Woodlock, David A. "Application of molecular mechanics polarization to fragment based drug design." Thesis, University of Essex, 2015. http://repository.essex.ac.uk/16774/.

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Polarization is a term that is often excluded from almost all virtual screening. Polarizability helps explain interactions between nonpolar atoms and electrically charged species. When studying fragments in FBDD these minor interactions could have large effect in changing how well a ligand will bind to its target. After including the polarizability terms in docking a validation set of ligands (Favia et al., 2011) with GLIDE, it improved the results the amount good docked poses (< 2 Å RMSD) by up to 12%. However some ligands were bound in incorrect poses. Further investigation was carried out w

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50

Rogers, Graeme W. "The development of sialidase inhibitors using structure-based drug design." Thesis, University of St Andrews, 2017. http://hdl.handle.net/10023/15516.

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Abstract:

The sialidases/neuraminidases represent a family of enzymes whose function is important in the pathogenicity of bacteria and the virulence of influenza. Relenza and Tamiflu represent two drugs that were developed using structure-based drug design (SBDD) and computational-assisted drug design (CADD). These drugs target the active site of the influenza neuraminidase A and B (GH-34 family). Sialidases in the GH-33 family could represent novel drug targets for the treatment of bacterial or parasitic infection. SBDD was employed to develop chemical tools of two GH-33 sialidases, NanB and TcTS. NanB

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