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Dissertations / Theses on the topic 'Small molecule-protein interactions'

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Published: 7 June 2025

Last updated: 16 July 2025

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1

Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.

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Thesis (Ph.D.)--Boston University<br>PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.<br>The binding of small molecules to a protein is among the most important phenomena in the chemistry of life; the activity and functionality of many proteins depend critically on binding small molecules. A deep

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2

Albertoni, Barbara [Verfasser]. "Biophysical analysis of protein-protein and protein-small molecule interactions / Barbara Albertoni." Bonn : Universitäts- und Landesbibliothek Bonn, 2011. http://d-nb.info/1044846909/34.

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3

Jackson, Matthew. "Assay development and investigation of small molecule and amyloid protein interactions." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6549/.

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4

Mittal, Sumit [Verfasser], Elsa [Gutachter] Sanchez-Garcia, and Simon [Gutachter] Ebbinghaus. "Small molecule modulation of protein-protein interactions / Sumit Mittal ; Gutachter: Elsa Sanchez-Garcia, Simon Ebbinghaus." Bochum : Ruhr-Universität Bochum, 2017. http://d-nb.info/1133361854/34.

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5

Nilsson, Jonas. "Design, Synthesis and Characterization of Small Molecule Inhibitors and Small Molecule : Peptide Conjugates as Protein Actors." Doctoral thesis, Linköpings universitet, Organisk Kemi, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-3943.

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This thesis describes different aspects of protein interactions. Initially the function of peptides and their conjugates with small molecule inhibitors on the surface of Human Carbonic Anhydrase isoenzyme II (HCAII) is evaluated. The affinities for HCAII of the flexible, synthetic helix-loop-helix motif conjugated with a series of spacered inhibitors were measured by fluorescence spectroscopy and found in the best cases to be in the low nM range. Dissociation constants show considerable dependence on linker length and vary from 3000 nM for the shortest spacer to 40 nM for the longest with a mi

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6

Fagiewicz, Robert Mateusz. "Structural analysis of protein-small molecule interactions by a crystallographic and spectroscopic approach." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2017. http://amslaurea.unibo.it/13892/.

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Modern spectroscopic techniques grant various methods for a protein structure determination among with a ligand interaction. This work aims at probing the structural insights of a protein-small molecule interaction with biocrystallography and optical spectroscopies. Two independent systems were investigated in the frame of this thesis. The first one involves flavoenzyme interaction with a natural nucleotide as a cofactor required for its catalytic activity and work was purely based on macromolecular crystallography. The second concerns incorporation of a synthetic fluorescent ligand into a mod

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7

Kung, Wei-Wei. "Protein-protein interactions and small molecule targeting of the multisubunit SOCS2-EloBC-Cul5-Rbx2 E3 ubiquitin ligase." Thesis, University of Dundee, 2018. https://discovery.dundee.ac.uk/en/studentTheses/b2dd4bc4-9a13-428b-a45a-bc46b1d9c116.

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The Cullin-RING E3 ligases (CRLs) are the largest subfamily of E3 ligases that participate in many biological processes determining the fate of proteins by catalysing ubiquitin transfer to specific substrates for proteasomal degradation. SOCS2 is a component of the multisubunit CRL E3 complex (CRL5SOCS2). SOCS2 plays important roles in several cancers and is involved in diabetes and inflammatory diseases. This work aims to understand the substrate recognition mechanism of SOCS2 at an atomic level and provides structural insights to guide the development of small-molecule tools and potential dr

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8

Wang, Lin. "DEVELOPMENT OF A NEW SCREENING AND DETECTION METHOD FOR IDENTIFYING PROTEIN-SMALL MOLECULE INTERACTIONS." OpenSIUC, 2014. https://opensiuc.lib.siu.edu/dissertations/861.

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Small molecules are known to play critical role in understanding most biological mechanisms of cells and organisms. Some examples, such as RNAs, peptides and drug molecules, etc., work by modulating cellular function, but with unknown modes. In most cases, these actions involve the small molecule interacting with proteins serving various functions. In recent years, much effort has been made in the investigation of interactions between small molecules (ligands) and target proteins. In our laboratory, a new technique termed Dynamic Isoelectric focusing Anisotropy Binding Ligand Assay (DIABLA) is

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9

Krumm, Stefanie A. [Verfasser], and Dieter [Akademischer Betreuer] Wolf. "Protein-protein and protein-small-molecule inhibitor interactions in the measles virus replication complex / Stefanie A. Krumm. Betreuer: Dieter Wolf." Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1069815470/34.

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10

Onel, Buket, and Buket Onel. "Promoter G-quadruplexes and their Interactions with Ligands and Proteins." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/621857.

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G-quadruplex secondary structures are four-stranded globular nucleic acid structures that form in specific DNA and RNA G-rich sequences with biological significance, such as those found in human telomeres, oncogene promoter regions, replication initiation sites, and 5’- and 3’-untranslated (UTR) regions, which have been identified as novel drug targets. The non-canonical G-quadruplex secondary structures readily form under physiologically relevant ionic conditions, and exhibit great diversity in their topologies and loop conformations depending on the DNA or RNA sequences at hand. The structur

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11

Iralde, Leire. "Design and synthesis of small-molecule stabilizers of protein-protein interactions (PPIs) as a novel class of therapeutic agents and basic reseach tool compounds." Doctoral thesis, Università di Siena, 2020. http://hdl.handle.net/11365/1094785.

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Protein-protein interactions (PPIs) mediate a wide variety of cellular processes, being essential for the regulation of most biological pathways. During the last years, targeting the PPIs complex network has been recognized as an emerging and promising drug discovery strategy for the therapeutic intervention of a number of pathologies. Here, we focus on the 14-3-3 adapter protein PPIs and its modulation through small molecules. This family of conserved proteins is expressed in all eukaryotic cells and maintains essential roles in regulatory processes by binding several hundred identified par

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12

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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13

Wadoos, Abdul. "Lysozyme-small molecule interactions." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264109.

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14

Fitzgerald, Ross Patrick. "Small molecule inhibitors of the p53-MDM2 protein-protein interaction." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/13136/.

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In Chapter 2, bis- and tris- arylsulfonamides, were investigated as possible inhibitors of the p53-MDM2 protein-protein interaction (PPI). The lead compound, 19, inhibited the PPI, in a fluorescence polarisation (FP) based competitive binding assay with ICso 26.4 pM and the most potent analogue, 66, with ICso 3 μM. The active compounds in this series, possess a 5-chloro-4-nitro-2-sulfonamoyl substituted thiophene ring that is very susceptible to SNAr reactions at the 5-position. Analogues of 19 and 66 were prepared to investigate the SAR of these inhibitors. No improvements in activity or stru

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15

Park, Chihyo. "Combinatorial design and synthesis of peptidomimics and small molecules for protein-protein interactions." Texas A&M University, 2006. http://hdl.handle.net/1969.1/4692.

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The solid phase combinatorial method is an excellent tool for the modulation of protein-protein interactions through focused library generations. Nucleophilic aromatic substitution reactions with an iodinated template on solid phase has opened a door for easy and pure libraries of 13-22 membered medium and macrocyclic peptidomimetics. These peptide mimics showed promising activities for tyrosine kinase receptors. Iodine functionality can then be used to modify the products, on the resin, via Sonogashira and Suzuki couplings and presumably through other organometallic catalysis. The coupled pro

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16

Lawrence, Charlotte. "Towards a small molecule inhibitor of the HIF-1/HIF-1 protein-protein interaction." Thesis, University of Southampton, 2015. https://eprints.soton.ac.uk/374783/.

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Hypoxia-inducible factor (HIF) is a heterodimeric, oxygen-dependent, transcription factor that regulates the cellular response to hypoxia by directing the expression of multiple genes, such as those involved in angiogenesis and glucose transport. HIF activation has been shown to aid the survival of cancer cells in hypoxic regions; hence it is viewed as a potentially important target for cancer therapy. There are two predominant isoforms of HIF, HIF-1 and HIF-2, formed by heterodimerisation of HIF-1 or HIF-2, respectively, with HIF-1. The dimerisation of the two subunits is necessary for DNA

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17

Kemp, Stuart James. "The design and synthesis of small molecule inhibitors of the MDM2-P53 protein-protein interaction." Thesis, University of Newcastle Upon Tyne, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.533699.

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18

Ong, Jennifer A. "Structure-based drug discovery of small molecule modulators of the protein-protein interaction between EGFR and PTP1B." Thesis, The University of Sydney, 2016. http://hdl.handle.net/2123/15887.

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Upregulation of epidermal growth factor receptor (EGFR) has been associated with numerous cancers such as those affecting the mammary glands, lungs and ovaries. We aimed to discover small molecule modulators which potentially promote the protein-protein interaction (PPI) between EGFR and protein tyrosine phosphatase 1B (PTP1B), which is known to dephosphorylate and inactivate the former, as a novel anticancer treatment. A combination of in silico (including protein-protein docking and structure-based virtual screening) and in vitro methods were employed to predict PPI structures and hit compou

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19

Sanchez, Perez Maria Concepcion. "Study of the N-terminal domains of MDM2 and MDM4, and their potential for targeting by small-molecule drugs." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/8763.

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The MDM2 and MDM4 oncoproteins are both involved in regulating the tumour suppressor, p53. While the MDM2–p53 interface is structurally and biophysically well characterised, the MDM4-p53 interaction has only recently attracted researchers’ attentions. The goal of this project was to establish structural and chemical ground rules for the disruption of the interactions between the N-terminal domains of MDM2/4 and p53, which is an attractive anticancer strategy. In the current work, successful recombinant production and purification protocols for both the N-terminal domains of MDM2 (i.e. MDM2-N,

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20

Zanella, S. "SYNTHESIS OF PEPTIDOMIMETIC LIGANDS TARGETING CELL-SURFACE RECEPTORS INVOLVED IN TUMOR ANGIOGENESIS." Doctoral thesis, Università degli Studi di Milano, 2017. http://hdl.handle.net/2434/473075.

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In the first part of the Thesis, the synthesis of different classes of peptidomimetics targeting integrin receptors is described. Both simple ligands and drug conjugates were synthesized and tested to assess their biological activity. In cancer therapy, peptides and peptidomimetics targeting integrins are employed as carriers to deliver cytotoxic drugs at the tumor site, taking advantage of integrin over-expression on the surface of tumor cells. Within this frame, synthetic efforts have been focused on the synthesis and on the conjugation to the cytotoxic agent paclitaxel of isoDGR-based integ

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21

Kinkade, Rebecca. "Rb-Raf-1 interaction as a therapeutic target for proliferative disorders." [Tampa, Fla] : University of South Florida, 2008. http://purl.fcla.edu/usf/dc/et/SFE0002426.

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22

Zhou, Li. "Small molecule inhibitors of protein-protein interactions." Thesis, 2016. https://hdl.handle.net/2144/14560.

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The development of orally bioavailable small molecule drugs targeting protein-protein interactions (PPIs) has been challenging1. Unlike conventional targets, PPIs’ extended, open surface makes it difficult for small molecules to bind. In order to achieve strong binding, it is frequently necessary to use larger molecules, which traditionally is considered to disfavor druglikeness2. However, PPIs possess great therapeutic potential due to their abundance and regulatory roles in cells3. More extensive studies are needed to identify larger chemotypes that retain good druglike properties and theref

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23

"Methods for Detection of Small Molecule-Protein Interactions." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.34938.

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abstract: Detection of molecular interactions is critical for understanding many biological processes, for detecting disease biomarkers, and for screening drug candidates. Fluorescence-based approach can be problematic, especially when applied to the detection of small molecules. Various label-free techniques, such as surface plasmon resonance technique are sensitive to mass, making it extremely challenging to detect small molecules. In this thesis, novel detection methods for molecular interactions are described. First, a simple detection paradigm based on reflectance interferometry

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24

Han, Xu. "Design and Synthesis of Small-Molecule Protein-Protein Interaction Antagonists." Thesis, 2014. http://hdl.handle.net/1805/6366.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>Protein-protein interactions play a crucial role in a wide range of biological processes. Research on the design and synthesis of small molecules to modulate these proteinprotein interactions can lead to new targets and drugs to modulate their function. In Chapter one, we discuss the design and synthesis of small molecules to probe a proteinprotein interaction in a voltage-gated Ca2+ channel. Virtual screening identified a compound (BTT-3) that contained a 3,4-dihydro-3,4’-pyrazole core. This compound had modest biological acti

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25

Ember, Brian. "Assay development and kinetic studies of protein-small molecule interactions." 2006. http://purl.galileo.usg.edu/uga%5Fetd/ember%5Fbrian%5F200605%5Fphd.

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26

Cavaco, Marco Calvinho. "Biologic-drug interactions between therapeutic protein and small-molecule drugs." Master's thesis, 2014. http://hdl.handle.net/10451/26782.

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Trabalho Final de Mestrado Integrado, Ciências Farmacêuticas, Universidade de Lisboa, Faculdade de Farmácia, 2014<br>Therapeutic proteins (TPs) are becoming extremely important as therapeutic agents. Refinements in molecular structure have warranted long-term administration with sig- nificantly increase on efficacy and adhesion to therapeutic regimens by the patients, broadening the scope of indications for this class of therapy. Therefore, some biologics have become the standard of care in several therapeutic areas, such as inflammatory and oncology. A consequence of the increasing biologics

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27

Chakraborti, Sohini. "Protein-small molecule interactions: Structural insights and applications in computational drug discovery." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5520.

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Deviation from normal healthy conditions, termed as disease, can often be triggered due to the malfunctioning of proteins. Modulating the functions of proteins by administering therapeutic agents (drugs) may alleviate the disease conditions. The majority of the drugs currently available in the market are small organic molecules due to their pharmacological and commercial advantages. These small molecule drugs interact with the protein targets through specific sites on the surface of the protein structure (binding sites). Thus, the structural data of protein-small molecule complexes forms a cru

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28

Chen, Shih-Hsun, and 陳世勳. "Small-molecule inhibitors of protein-protein interactions selectively induce chemoresistant/caspase-3-deficient cancer cell death." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/17589166788216123598.

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博士<br>國立交通大學<br>生物科技系所<br>102<br>Protein-protein interactions (PPIs) are essential for biological processes and thus often considered as potentially pharmaceutical drug targets. Targeting the interfaces between proteins has huge therapeutic potential, but discovering small-molecule drugs which block PPIs is an enormous challenge currently. According to our previous studies, β-tubulin:CCT-β complex can serve as an effective chemotherapeutic target for treating clinical tubulin-binding agent-resistant or CCT-β-overexpressing tumors and disrupting XIAP:CASP7 complex represents an effective an

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29

Grant, Stephen Nicholas. "Investigation of Some Small Molecule-Protein and Protein-Protein Interactions in Nicotine Addiction, Opioid Use Disorder, and COVID-19." Thesis, 2022. https://thesis.library.caltech.edu/14302/1/Thesis%20Stephen%20Grant%20Final_v2.pdf.

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<p>Nicotine addiction, opioid use disorder, and COVID-19 have made lasting impacts on every aspect of society. These are complicated conditions, and studies in these fields will likely continue for decades, if not centuries. Here, we make contributions to each of these issues using electrophysiology and microscopy. The first chapter goes into the motivation behind this thesis and the major experiments I used in my graduate career. In the second chapter, we introduce a new amino acid into the mouse muscle nicotinic acetylcholine receptor in an attempt to understand the dynamics of receptor acti

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30

Mishra, Akaash K. "Developing small molecule inhibitors targeting Replication Protein A for platinum-based combination therapy." Thesis, 2014. http://hdl.handle.net/1805/6466.

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Indiana University-Purdue University Indianapolis (IUPUI)<br>All platinum (Pt)-based chemotherapeutics exert their efficacy primarily via the formation of DNA adducts which interfere with DNA replication, transcription and cell division and ultimately induce cell death. Repair and tolerance of Pt-DNA lesions by nucleotide excision repair and homologous recombination (HR) can substantially reduce the effectiveness of the Pt therapy. Inhibition of these repair pathways, therefore, holds the potential to sensitize cancer cells to Pt treatment and increase clinical efficacy. Replication Protein

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31

Almaraz, Elky. "The Interactions of Zinc Thiolate Complexes and Exogenous Metal Species: Investigations of Thiolate Bridging and Metal Exchange." 2009. http://hdl.handle.net/1969.1/ETD-TAMU-2009-05-536.

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Small molecule Zn(II) complexes containing N- and S- donor environments may serve as appropriate models for mimicking Zn protein sites, and thus, their reactions with heavy metal ions such as Pt(II) and W(0) may provide insight into possible adduct formation and zinc displacement. To study such possible interactions between zinc finger proteins and platinum-bound DNA, the ZnN2S2 dimeric complex, N,N?-bis(2- mercaptoethyl)-1,4-diazacycloheptane zinc (II), [Zn-1?]2, has been examined for Znbound thiolate reactivity in the presence of Pt(II) nitrogen ? rich compounds. The reactions yielded Zn/Pt

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32

Huang, Han-Tsung, and 黃漢聰. "Epitope Mapping for Protein-Small Molecule Interaction by Nanoprobe-Based Affinity Mass Spectrometry." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/29641948397711215356.

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碩士<br>國立臺灣海洋大學<br>生物科技研究所<br>95<br>Abstract Molecular recognition plays an important regulator in cellular activities. Mapping the interaction sites of protein is of great interest since it contributes much to our understanding of the mechanisms of molecular recognition and provides the basis for rational vaccine design. We employed Nanoprobe-Based Affinity Mass Spectrometry (NBAMS) to rapidly and accurately map small molecule/protein interaction sites. To demonstrate the general applicability of our approach in tackling of small molecule/protein interaction, three biomolecular interaction sys

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33

Surmiak, Ewa. "Small-molecule inhibitors of the Mdm2-p53 protein-protein interaction: substituted 1,5-dihydro-2H-pyrrol-2-ones and tetrazoles." Praca doktorska, 2015. https://ruj.uj.edu.pl/xmlui/handle/item/45023.

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34

Shahani, Vijay Mohan. "An Exploration into the Molecular Recognition of Signal Transducer and Activator of Transcription 3 Protein Using Rationally Designed Small Molecule Binders." Thesis, 2013. http://hdl.handle.net/1807/43719.

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Signal transducer and activator of transcription 3 (STAT3) is a cancer-driving proto-oncoprotein that represents a novel target for the development of chemotherapeutics. In this study, the functional requirements to furnish a potent STAT3 inhibitor was investigated. First, a series of peptidomimetic inhibitors were rationally designed from lead parent peptides. Prepared peptidomimetics overcame the limitations normally associated with peptide agents and displayed improved activity in biophysical evaluations. Notably, lead peptidomimetic agents possessed micromolar cellular activity which was u

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35

Antonschmidt, Leif. "On the molecular basis of α-synuclein aggregation on phospholipid membranes in the presence and absence of anle138b". Doctoral thesis, 2019. http://hdl.handle.net/21.11130/00-1735-0000-0005-1428-8.

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