Дисертації з теми "Protein-small molecule interactions"
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Napoleon, Raeanne L. "Understanding small molecule-protein interactions." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31592.
Повний текст джерелаPLEASE 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.
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 understanding of protein-small molecule interactions and the interplay between ligation and function can give valuable insight into key systems of interest. The complete characterization of any small molecule-protein interaction requires quantification of many interactions and the pursuit of such information is the purpose of this body of work. The discovery of binding regions on proteins, or "hot spots," is an important step in drug development. To this end, a highly regarded and robust fragment-based protocol has been developed for the detection of hot spots. Firstly, we use this protocol in conjunction with other computation techniques, such as homology modeling, to locate the allosteric binding site of £-phenylalanine in Phenylalanine Hydroxylase. Secondly, computational fragment mapping was employed to locate the site of allostery for Ras, an important signaling protein. Lastly, the identification of hot spots for many unligated protein targets is presented highlighting the importance of a reliable way to predict druggability computationally. The second part of this dissertation shifts focus to the development of electrostatic models of small molecules. It is widely believed that classical potentials can describe neither vibrational frequency shifts in condensed phases nor the response of vibrational frequencies to an applied electric field, the vibrational Stark effect. In this work, an improved classical molecular electrostatic model for the CO ligand was developed to faithfully model these phenomena. This model is found to predict the vibrational Stark effect and Fe-CO binding energy with unprecedented accuracy for such a classical model. As an extension of this work, a geometrically dependent water potential was developed. This work has shown that comparison of results obtained from current water models against experimentally determined proton momentum distributions is an invaluable benchmark
2031-01-01
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.
Повний текст джерелаPark, 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.
Повний текст джерелаJackson, Matthew. "Assay development and investigation of small molecule and amyloid protein interactions." Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6549/.
Повний текст джерелаMittal, 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.
Повний текст джерелаNilsson, 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.
Повний текст джерелаFagiewicz, 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/.
Повний текст джерелаKung, 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.
Повний текст джерелаWang, Lin. "DEVELOPMENT OF A NEW SCREENING AND DETECTION METHOD FOR IDENTIFYING PROTEIN-SMALL MOLECULE INTERACTIONS." OpenSIUC, 2014. https://opensiuc.lib.siu.edu/dissertations/861.
Повний текст джерелаKrumm, 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.
Повний текст джерелаOnel, 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.
Повний текст джерелаIralde, 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.
Повний текст джерелаBarelier, 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.
Повний текст джерелаFragment-Based Drug Design (FBDD) has been proposed in 1996 and has since been recognized as a tangible alternative to the more classical drug discovery methods such as High-Throuput Screening. FBDD consists of screening a small number (< 10 000) of low-molecular weight (< 300 Da) compounds and detect those that bind to the target (protein or nucleic acids). Because of their low complexity, fragment molecules usually display low affinities for their target, hence detecting fragment-protein interactions is mostly achieved using a biophysical technique (mostly Nuclear Magnetic Resonance (NMR), X-ray crystallography or Surface Plasmon Resonance). “Hit” fragments are then modified by addition of chemical substituents, or linked together, so as to elaborate a more complex molecule, forming more interactions with the target and hence displaying an improved affinity. As compared to the more classical High Throughput Screening method, fragment screening provides several advantages, including a better exploration of chemical space, highly ligand-efficient hits and easier optimization of the hits into more affine molecules. In this PhD project, several aspects of FDBB have been addressed : first, FBDD approaches were applied to the research of an inhibitor of the human peroxiredoxin 5 protein, using NMR not only as a screening method but also for the characterization of the protein-fragment interactions. The discovery of an inhibitor against this enzyme would allow to better understand its function. Next, methodological aspects of the FBDD method were addressed : Do fragments conserve their binding site, binding efficiency and mode of interaction upon optimization? Can the fragments display specificity towards a given target? Towards a given binding site? These issues, rarely studied, are yet essential to the understanding of the behavior of fragment molecules, and will be addressed firstly by defragmentating several Bcl-xL inhibitors into fragments and studying their behavior towards the protein in terms of a_nity and binding mode, secondly by screening a set of fragments against five different proteins (human peroxiredoxin 5, human serum albumin and three homologous proteins of the Bcl-2 family of proteins). More generally, this PhD project aims at studying less characterized aspects of the fragment methodology and proposing answers to better understand the behavior of fragment molecules towards their targets, both in the initial screening step and then during their optimization
Wadoos, Abdul. "Lysozyme-small molecule interactions." Thesis, University of Glasgow, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.264109.
Повний текст джерелаFitzgerald, Ross Patrick. "Small molecule inhibitors of the p53-MDM2 protein-protein interaction." Thesis, University of Nottingham, 2011. http://eprints.nottingham.ac.uk/13136/.
Повний текст джерелаYen, Li-Hsuan. "Inhibition of protein-peptide interactions by small molecules." Thesis, University of Edinburgh, 2014. http://hdl.handle.net/1842/9978.
Повний текст джерелаLawrence, 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/.
Повний текст джерелаMotto, I. M. "Targeting protein/protein interactions with small molecules : structure based design of pro-apoptotic peptidomimetics." Doctoral thesis, Università degli Studi di Milano, 2007. http://hdl.handle.net/2434/42452.
Повний текст джерелаSanchez, 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.
Повний текст джерелаKemp, 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.
Повний текст джерелаCollier, Miranda. "Small heat shock protein interactions with in vivo partners." Thesis, University of Oxford, 2018. http://ora.ox.ac.uk/objects/uuid:24cf8041-c82d-4bc4-87a7-0ae7e38f1879.
Повний текст джерелаSeco, Martins Marques Neves João Filipe. "NMR study of 14-3-3 protein-protein interactions and modulation thereof by small molecules." Thesis, Lille, 2019. http://www.theses.fr/2019LIL1S108.
Повний текст джерела14-3-3 proteins are adapter proteins that exert their biological functions by modulating the activity of hundreds of proteins. This remarkable interactome makes 14-3-3 proteins influent actors in many cellular events and, by consequence, in several pathologies. The selective stabilization or inhibition of 14-3-3 protein-protein interactions (PPIs) are therefore seen as promising approaches for finding innovative therapies for a number of conditions like Alzheimer’s, cancer or Parkinson. Our first objective towards finding small molecule modulators of these targets was to obtain the molecular detail of 14-3-3 PPIs. To this end, using Nuclear Magnetic Resonance (NMR), we assigned the backbone chemical shifts of 14-3-3σ. We then studied the 14-3-3/phosphorylated Tau interaction and found that Tau binds strictly within the amphipathic binding grove of 14-3-3 and can anchor in both monomers of the 14-3-3 dimer. We also studied the 14-3-3/p53 interaction and showed by NMR, that intramolecular interactions within the peptide define a conformation that drives the affinity towards 14-3-3. 2019We then focused on the optimization of NMR assays for screening and characterization of the effect of small-molecules binding to 14-3-3 or 14-3-3 complexes with target’s phosphopeptides. We used, for example, phospho-mimetic peptides to inhibit the Tau/14-3-3 interaction. In a different strategy, we screened a fragment library against 14-3-3σ and found three hits binding to different regions of the protein. Using our NMR assays we further characterized small molecules binding 14-3-3 complexes with, for example, p53 and p65 peptides and demonstrated the stabilization capacity of some compounds
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.
Повний текст джерелаPrischich, Davia. "Development and applications of photoswitchable small molecules and peptides to control protein-protein interactions and GPCR activity." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/671019.
Повний текст джерелаLa fotofarmacología es una técnica muy prometedora que permite controlar con luz y de manera reversible Ia actividad de compuestos activos biológicamente. En esta tesis doctoral hemos desarrollado péptidos y ligandos fotoconmutables para regular las interacciones entre proteínas y Ia actividad de receptores acoplados a proteínas G (GPCRs). En primer Iugar, validamos Ia actividad de TL2, un péptido fotoconmutable que inhibe Ia endocitosis mediada por clatrina, en un modelo simple de célula eucariota, Ia levadura Saccharomyces cerevisiae. Mediante Ia tecnica de "kimografía" en esferoplastos que expresan el marcador fluorescente GFP-Sia1, caracterizamos el efecto de TL2 en este proceso celular y su posible mecanismo de acción. Luego aplicamos Ia estrategia de diseño de TL2 para crear una librería de péptidos que inhiben o activan con luz Ia vía de señalización mediada por Wnt/β-catenina. Tras su caracterización química y fotocrómica, analizamos el efecto de los ciclos de luz sobre las estructuras secundarias de los péptidos y su union a Ia β-catenina. Para evaluar su actividad, empleamos un ensayo de luminiscencia que permite cuantificar Ia expresión génica y ponemos a punto un modelo in vivo de regeneración de tejidos en planarias Schmidtea mediterranea. A continuación, ampliamos las aplicaciones de los péptidos fotoconmutables desde Ia inhibición de las interacciones proteína-proteína descrita anteriormente, a Ia activación de receptores de neuropéptidos como las orexinas. En particular, creamos un análogo fotoconmutable de Ia orexina insertando un aminoácido con un grupo azobenceno en Ia secuencia lineal del péptido. Validamos este nuevo diseño mediante estudios estructurales de dicroísmo circular y modelado molecular, y su actividad mediante Ia medida de señales intracelulares como el calcio. Por ultimo,diseñamos y sintetizamos varios derivados fotoconmutables de ligandos α-adrenergicos insertando azoheteroarenos en sus estructuras. Mediante ensayos de unión evaluamos Ia afinidad de los compuestos hacia los adrenoreceptores de tipo α,y comprobamos su activad en un modelo de reactividad vascular en aorta de rata. Uno de los compuestos permitió manipular Ia motilidad de peces cebra y el tamaño pupilar en ratones, demostrando por primera vez el control de los adrenoreceptores con luz in vivo.
Misale, Antonio. "Synthesis of angucycline-based small molecules as potential STAT3 : STAT3 protein-protein interaction inhibitors for cancer therapy." Thesis, University of London, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.555844.
Повний текст джерелаAlsabban, Abdulrahman Essam. "Establishing methods to screen novel small molecules targeting insulin-like growth factor/insulin-like growth factor binding protein interaction." Thesis, University of British Columbia, 2013. http://hdl.handle.net/2429/45046.
Повний текст джерелаTimmoneri, Martina. "Inhibition of HCMV replication by small molecules interfering with the dimerization of the DNA polymerase processivity factor UL44." Doctoral thesis, Università degli studi di Padova, 2018. http://hdl.handle.net/11577/3425876.
Повний текст джерелаCytomegalovirus (CMV) è un importante patogeno di interesse umano. Al momento gli antivirali disponibili ed utilizzati per la terapia contro l’infezione da CMV presentano una serie di problematica quali l’alto costo, bassa biodisponibilità, alta tossicità ed il presentarsi di ceppi virali resistenti. Inoltre non è disponibile un vaccino ed ancora non è stato approvato alcun farmaco per prevenire la trasmissione verticale durante la gravidanza. Per questi motivi, sono necessari nuovi efficaci farmaci antivirali. La proteina accessoria UL44 della DNA polimerasi di CMV, svolge un ruolo essenziale nella replicazione virale, conferendo processività alla subunità catalitica UL54 ancorando il complesso oloenzimatico al DNA. Il legame di UL44 al dsDNA avviene in assenza di ATP e dei clamp loaders, e dipende dalla omodimerizzazione di UL44. Il nostro gruppo di ricerca, infatti ha recentemente dimostrato che la proteina può dimerizzare in cellule e che mutazioni puntiformi in grado di inficiare tale dimerizzazione prevengono il legame con il DNA ed aboliscono la replicazione del DNA virale oriLyt-dipendente in saggi di transcomplementazione transiente. Perciò, la distruzione dell’omodimerizzazione UL44 rappresenta un potenziale ed allettante target per lo sviluppo di nuovi antivirali. Partendo da queste osservazioni ed usando la struttura cristallografica degli omodimeri UL44 che è stata recentemente pubblicata, il nostro gruppo di ricerca ha eseguito un virtual screening con il software Glide in combinazione con una libreria di 1.3 x 10^6 piccole molecole (SMs) per identificare SMs che potenzialmente potessero interferire con l’omodimerizzazione di UL44. Dopo tre rounds di screening (HTVS: high-throughput virtual screening, SP: standard precision, XP: extra precision), seguiti da un’analisi delle proprietà chimiche dei composti, sono state selezione 18 SM per ulteriori analisi. I composti selezionati sono stati acquistati presso un fornitore commerciale, per essere testati in diversi saggi per valutare le loro abilità di inibire l’omodimerizzazione di UL44 in vitro, sia la replicazione virale. Con questo scopo, abbiamo utilizzato due metodi in vitro per monitorare l’effetto dei nostri candidati sulla dimerizzazione di UL44, quali GST-pulldown assay e Thermal Shift Assay (TSA). Inoltre per studiare l’inibizione sulla replicazione virale sono stati eseguiti saggi di Plaque Reduction Assay (PRA) e Fluorescence Reduction Assay (FRA). Inizialmente abbiamo confermato che il GST-pulldown assay fosse idoneo per studiare la dimerizzazione di UL44 e la sua perturbazione causata dalle SMs. Pertanto abbiamo eseguito un primo screening per saggiare l’effetto delle 18 SMs sulla dimerizzazione di UL44, ed abbiamo identificato 3 molecole che inibivano la dimerizzazione in modo riproducibile. Incoraggiati da questi risultati, abbiamo selezionato queste SMs per valutare una possibile relazione dose-risposta tra l’inibizione della dimerizzazione e la concentrazione dei composti. Sfortunatamente, l’analisi dei dati hanno rivelato alta variabilità, e perdita di correlazione tra l’inibizione e la concentrazione delle SMs utilizzate nei saggi. In parallelo, abbiamo eseguito PRAs per validare l’effetto delle SMs precedentemente selezionate, ma queste si sono presentati incapaci di inibire la replicazione virale in modo consistente. Successivamente abbiamo ottenuto due virus CMV ricombinanti (TB4-IE2-EYFP and TB4-UL83-EYFP) da Michael Winkler (Leibniz-Institut für Primatenforschung Goettingen, Germany) per studiare l’effetto delle nostre molecole sulla replicazione di CMV mediante FRAs. Pertanto, dopo uno screening delle 18 SMs, 4 di queste sono state identificate come possibili inibitori della replicazione virale e sono state selezionate per essere ulteriormente studiate. Abbiamo valutato la loro dose effettiva 50% (ED50) e la loro concentrazione citotossica 50% (CC50) e gli effetti relativi all’espressione genica. Solo due SMs in modo riproducibile inibivano l’espressione dei geni Early e Late. Poi abbiamo valutato un saggio in vitro alternativo e tra le varie possibilità, abbiamo scelto il TSA che è un saggio in grado di informare se una SM induce la distruzione delle interfacce di un oligomero costitutivo. In un primo momento abbiamo confermato che il saggio permettesse la discriminazione tra le forme monomeriche e dimeriche di UL44, suggerendo il suo potenziale per lo screening delle nostre SMs. Come risultato di questo screening, una molecola ha rivelato possibile inibizione della dimerizzazione.
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.
Повний текст джерелаLangston, Kelsey Murphey. "Identification of the Binding Partners for HspB2 and CryAB Reveals Myofibril and Mitochondrial Protein Interactions and Non-Redundant Roles for Small Heat Shock Proteins." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/3822.
Повний текст джерелаUryga-Polowy, Viviane [Verfasser]. "Development of a labeling strategy for the synthesis of fluorescent libraries of peptides and small molecules and their use in fluorescence-based binding assays for the study of protein-protein interactions / Viviane Uryga-Polowy." Berlin : Freie Universität Berlin, 2009. http://d-nb.info/1023958619/34.
Повний текст джерелаDi, Antonio Veronica. "Towards the identification of small molecules inhibiting he dimerization of HCMV DNA polymerase processivity factor UL44." Doctoral thesis, Università degli studi di Padova, 2017. http://hdl.handle.net/11577/3423139.
Повний текст джерелаCytomegalovirus (CMV) è un importante patogeno di interesse umano. Al momento gli antivirali disponibili ed utilizzati per la terapia contro l’infezione da CMV presentano una serie di controindicazioni dovute all’alto costo, bassa biodisponibilità, alta tossicità ed il presentarsi di ceppi virali resistenti. Inoltre non è disponibile un vaccine ed ancora non è ancora stato approvato l’uso di alcun farmaco per prevenire la trasmissione verticale durante la gravidanza. Per questi motivi, sono necessari nuovi ed efficaci farmaci antivirali. La proteina accessoria UL44 della DNA polimerasi di CMV, svolge un ruolo essenziale nella replicazione virale, conferendo processività alla subunità catalitica UL54 ancorando il complesso oloenzimatico al DNA. Il legame di UL44 al dsDNA avviene in assenza di ATP e dei clamp loaders, e dipende dalla omodimerizzazione di UL44. Infatti, il nostro gruppo di ricerca ha recentemente dimostrato che la proteina può dimerizzare in cellule e che mutazioni puntiformi in grado di inficiare tale dimerizzazione prevengono il legame con il DNA ed aboliscono la replicazione del DNA virale oriLyt-dipendente in saggi di transcomplementazione transiente. Perciò, la distruzione dell’omodimerizzazione UL44 rappresenta un potenziale allettante bersaglio per lo sviluppo di nuovi anti-virali. Partendo da queste osservazioni ed usando la struttura cristallografica recentemente pubblicata degli omodimeri UL44, il nostro gruppo di ricerca ha eseguito un virtual screening con il software Glide in combinazione con una libreria di 1.3 x 10^6 piccole molecole (SMs) per identificare SMs che potenzialmente potessero interferire con l’omodimerizzazione di UL44. Dopo tre rounds di screening (HTVS: high-throughput virtual screening, SP: standard precision, XP: extra precision), seguiti da un’analisi delle proprietà chimiche dei composti, sono state selezione 18 SM per ulteriori analisi. I composti selezionati sono stati acquistati presso un fornitore commerciale, per essere testati in diversi saggi per valutare le loro abilità di inibire l’omodimerizzazione di UL44, sia in cellule che in vitro. A questo scopo, abbiamo utilizzato diversi saggi in cellule e in vitro per monitorare l’effetto delle SMs sulla dimerizzazione di UL44. Nei saggi cellulari, le tecniche utilizzate includono Fluorescent Resonant Energy Transfer (FRET) e Bioluminescence Resonant Energy Transfer (BRET), mentre per saggi in vitro è stato utilizzato il saggio GST-pull down. I nostri dati indicano che la metodica FRET acceptor photobleaching è in grado di rilevare sia l’omodimerizzazione di UL44, sia il legame con il dominio C-terminale della subunità catalitica (residui 1125-1242). Queste interazioni sono sensibili all’introduzione di mutazioni puntiformi che alterano i due processi, evidenziando la specificità di questa tecnica. Siamo stati quindi in grado di confermare che UL44 forma dimeri in un contesto cellulare. Purtroppo, l’acquisizione dei dati e la loro analisi richiedono un lungo tempo e dipendono da alti livelli di espressione delle proteine di fusione. Per contro, il saggio BRET permette un rapido e preciso monitoraggio quantitativo dell’omodimerizzazione di UL44 e il legame con UL54 in cellule viventi. Inoltre, attraverso esperimenti di saturazione, che permettono di calcolare in modo preciso i valori di Bmax e B50 relative all’omodimerizzazione o al legame con UL54 per varianti di UL44 che contengono singole sostituzioni amminoacidiche che affliggono la dimerizzazione di UL44, il suo legame a UL54 o il DNA, nonché il trasporto al nucleo della proteina. I dati ottenuti possono aiutare a comprendere il processo di formazione dell’oloenzima della DNA polimerasi di CMV, suggerendo cambiamenti conformazionali nel complesso olenzimatico in seguito a legame con il DNA. Inoltre, il calcolo di Bmax e B50 è stato usato per sviluppare tre differenti sistemi cellulari esprimenti un’ideale quantità di UL44 da utilizzare come piattaforma per lo screening di SM, poiché sono in grado di generare valori di BRET ratio simili al 50% della Bmax .Questi includono un sistema di espressione completamente stabile, in cui sia RLuc-UL44 che YFP-UL44 sono stabilmente espresse in cellule derivate da HEK293 A, un sistema ibrido stabile/transiente, in cui YFP-UL44 è stabilmente espressa e RLuc-UL44 è espressa in transiente, o un sistema completamente transiente in cui entrambe le proteine sono espresse transientemente. Saggi di competizione eseguiti sovra-esprimendo quantità crescenti di UL44 fusa a un FLAG tag hanno evidenziato che nessun inibizione può essere ottenuta per il sistema completamente stabile, probabilmente per la difficoltà di distruggere un complesso proteico preformato piuttosto che prevenirne la formazione. Per questo motive ci siamo focalizzati su sistemi transienti di espressione piuttosto che sul sistema interamente stabile. Sulla base di questi dati, un primo screening su piccolo scala è stato eseguito per studiare l’effetto di 18 SMs sulla dimerizzazione di UL44 usando il sistema BRET stabile/transiente. Le 18 piccole molecole sono state risospese in DMSO e la loro tossicità è stata valutata in coltura cellulare, prima di essere aggiunte a concentrazioni subtossiche alla linea YFP-UL44, sei ore dopo la trasfezione per esprimere RLuc-UL44. La nostra analisi ha identificato solo composti che inibivano blandamente il BRET ratio relativo alla dimerizzazione di UL44. Per questo motivo abbiamo ri-valutato il set up del saggio BRET, diminuendo il tempo d’incubazione delle SM prima di testare i valori BRET da 42 a 18 ore, utilizzando un saggio completamente transiente e diminuendo la quantità di proteine espresse. Per quest’ultima è stato necessario cambiare il substrato utilizzato per generare il segnale bioluminescente da CTZ a hCTZ. È stato eseguito un nuovo screening, con risultati molto simili a quelli ottenuti utilizzando il setup originale. Inoltre, quando i candidati migliori sono stati rivalutati usando un controllo negativo, il loro effetto sul BRET ratio è risultato aspecifico. Ulteriormente, la BRET, come la FRET, non è riuscita a rilevare uno specifico effetto nell’interazione UL44/UL54 di una SM in grado di distruggere questa interazione. Possiamo quindi concludere che BRET e FRET non sono tecniche ideali per la ricerca di SM inibitrici dell’interazione tra le proteine. Ci siamo poi focalizzati su metodi in vitro, partendo dal saggio GST-pull down, il quale è stato effettato utilizzando il dominio C-terminale (residui 1-290) di UL44, fuso o con GST o con 6His-tag. I risultati ottenuti mostrano che la tecnica GST-pull down è in grado di rilevare differenze nel legame tra UL44 wild-type e i mutanti con mutazioni nel sito di dimerizzazione, suggerendo una possibile applicazione di GST-pull down per lo screening delle SMs. Questa tecnica è stata implementata per questo studio, e i dati preliminari suggeriscono che il numero di SMs testate potrebbe portare all’inibizione della dimerizzazione di UL44. In conclusione, abbiamo sviluppato diversi saggi per monitorare la dimerizzazione di UL44. I saggi cellulari basati su RET confermano che UL44 forma dimeri in cellule viventi, e dimostrano di essere subottimali per lo screening. D’altro canto, i metodi in vitro come GST-pull down dimostrerebbero un maggiore sensibilità e sono stati implementati per l’identificazione degli inibitori della dimerizzazione di UL44.
Yasmin, Lubna. "Exoenzyme S of Pseudomonas aeruginosa : cellular targets and interaction with 14-3-3." Doctoral thesis, Umeå : Univ, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-1411.
Повний текст джерелаKinkade, 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.
Повний текст джерелаChan, Yao Chong Maud. "Structure et dynamique de protéines intrinsèquement désordonnées : Caractérisation par une approche combinant dynamique moléculaire avancée et SAXS." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS257.
Повний текст джерелаThe PhD work will consist in exploring and characterizing the conformational ensemble of intrinsically disordered proteins (IDPs), by using several complementary methods, including enhanced molecular dynamics simulations and small angle X-ray scattering (SAXS). IDPs are proteins having one or several regions that lack stable secondary structures in the unbound state, but which can adopt various structured conformations to bind other proteins. In the case of three IDPs, the project aims to answer the question of whether these secondary structures formed at the protein-protein interfaces transiently pre-exist or not in the unbound state of solvated IDPs. If it is possible to identify and characterize these molecular recognition features (MoRFs) in the IDP unbound state, then the results of this work will subsequently help to determine the structures of protein complexes involving IDPs
Zhou, Li. "Small molecule inhibitors of protein-protein interactions." Thesis, 2016. https://hdl.handle.net/2144/14560.
Повний текст джерела"Methods for Detection of Small Molecule-Protein Interactions." Doctoral diss., 2015. http://hdl.handle.net/2286/R.I.34938.
Повний текст джерелаDissertation/Thesis
Doctoral Dissertation Electrical Engineering 2015
Han, Xu. "Design and Synthesis of Small-Molecule Protein-Protein Interaction Antagonists." Thesis, 2014. http://hdl.handle.net/1805/6366.
Повний текст джерелаProtein-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 activity when tested in a fluorescence polarization (FP) assay. The synthetic route to BTT-3 consisted of six steps. In addition, analogs of BTT-3 were made for a structure-activity study to establish the importance of a carboxylate moiety. We also synthesized a biotinylated benzophenone photo-affinity probe and linked it to BTT-3 to identify additional protein targets of the compound. In Chapter two, small-molecule antagonists targeting uPA-uPAR protein-protein interaction are presented. A total of 500 commercially-available compounds were previously identified by virtual screening and tested by a FP assay. Three classes of compounds were found with biological activity. The first class of compounds contains pyrrolidone core structures represented by IPR- 1110, the second class has a novel pyrrolo[3,4-c]pyrazole ring system, represented by xv IPR-1283 and the last series had compounds with a 1,2-disubstituted 1,2- dihydropyrrolo[3,4-b]indol-3(4H)-one core structure, represented by IPR-540. Each of these three compounds were synthesized and assessed by FP and ELISA assays. A binding mode of IPR-1110 with uPA was subsequently proposed. Based on this binding mode, another 61 IPR-1110 derivatives were synthesized by us to illustrate the SAR activity. Analogs of the other two series were also synthesized.
Ember, Brian. "Assay development and kinetic studies of protein-small molecule interactions." 2006. http://purl.galileo.usg.edu/uga%5Fetd/ember%5Fbrian%5F200605%5Fphd.
Повний текст джерелаCavaco, Marco Calvinho. "Biologic-drug interactions between therapeutic protein and small-molecule drugs." Master's thesis, 2014. http://hdl.handle.net/10451/26782.
Повний текст джерелаTherapeutic 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 indications is the concomitant administration with well-established small-molecule drugs (sMDs). Patent expiration of several biologics, such as monoclonal Antibodies (mAbs), may also contribute to the in- creasing use of TPs since biossimilars become available at more appealing prices. A bet- ter understanding of biologic-drug interactions (BDIs) is necessary to avoid the decrease of therapeutic regimens efficacy. By the existing regulatory guidance, the development of a new sMD includes an evaluation of the potential drug-drug interactions (DDIs) for concomitant medications. Only a few drug interaction studies have been performed with macromolecules since those studies, involving TPs, are inherently complicated. Few clinically relevant animal models available, long elimination half-lives, and complex elim- ination pathways, which differ from the classical cytochrome P450 (CYP450) system, are among the expected difficulties. In spite of the pharmacokinetic (PK) interactions, the most important and well-studied mechanism of interaction, pharmacodynamics (PD) in- teractions may also represent a possible explanation for several BDIs. The present re- view of the current literature encompasses several BDIs involving TPs (either as perpe- trators or as victims) and their specific mechanism of interaction.
Chakraborti, Sohini. "Protein-small molecule interactions: Structural insights and applications in computational drug discovery." Thesis, 2021. https://etd.iisc.ac.in/handle/2005/5520.
Повний текст джерелаDST-INSPIRE fellowship
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.
Повний текст джерела國立交通大學
生物科技系所
102
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 and safe novel strategy for selectively killing CASP3-deficent cancer cells. We have developed a novel multiple-sites (or modes) virtual screening strategy with site-moiety maps to discover small molecules which can be simultaneously fitted into multiple sites (or modes) to disrupt PPIs. Moreover, we identified three key residues in CCT-β, K250, F252 and R293, which play an important role in interacting with β-tubulin and binding of the small molecules to I-Lys site induces disassociation of XIAP:CASP7 through an allosteric mechanism. Our method discovers the first potent and non-covalent inhibitor, R379603, efficiently induces apoptosis of HEK-293 cells with an EC50 at 4.6 M via targeting two previously uncharacterized and independent sites to block β-tubulin:CCT-β interface and triggering caspase-dependent signaling cascades. Notably, R379603 causes a more severe apoptosis of paclitaxel-resistant MCF-7 breast cancer cells in vitro and in cultured cells due to an increased level of CCT-β as compared with its parental MCF-7 cells. We also discovered a small molecule inhibitor (643943) which can reversibly bind to I-Lys site, an allosteric site away from the interface of the linker region between BIR1 and BIR2 domains of XIAP and CASP7 active site. This compound thus releases XIAP constraint and activated CASP7 to selectively kill CASP3 down-regulated (CASP3/DR) cancer cells. Besides, 643943 effectively sensitizes chemo-resistant cancer cells to chemotherapy at a low-micromolar concentration (≦5 μM). We believe that multiple-sites (or modes) strategy provides an alternative and useful method for discovering potential inhibitors and binding mechanisms for pharmaceutical targets.
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.
Повний текст джерелаNicotine 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 activation. In the third chapter, we continue the Lester lab’s work on the neuroscientific effects of menthol and how it plays a role in nicotine addiction. We found the binding site for menthol on the α4β2 nicotinic acetylcholine receptor, which continues our hypothesis that the neuroscientific effects of menthol are detrimental to cigarette smokers. Fortunately, partly because of our studies, mentholated nicotine products are being phased out of the United States. The fourth and fifth chapters investigate μ-opioid receptor trafficking, both the trafficking from the endoplasmic reticulum and endocytosis from the plasma membrane. Both of these events play a role in inducing opioid use disorder and increasing the danger of using opioids. We hope that these studies will help other researchers understand opioid use disorder and fight the opioid epidemic. Finally, we studied the effects of SARS-COV-2 proteins on epithelial sodium channels. These channels are important for regulating lung fluid levels where their improper function may cause pulmonary edema. Pulmonary edema has been observed in COVID-19 patients. Altogether, we believe that we have made meaningful impacts on these important health concerns in this thesis. We look forward to how the scientific communities continue to build on our results.
Mishra, Akaash K. "Developing small molecule inhibitors targeting Replication Protein A for platinum-based combination therapy." Thesis, 2014. http://hdl.handle.net/1805/6466.
Повний текст джерелаAll 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 A (RPA) plays essential roles in both NER and HR, along with its role in DNA replication and DNA damage checkpoint activation. Each of these functions requires RPA binding to single-stranded DNA (ssDNA). We synthesized structural analogs of our previously reported RPA inhibitor TDRL-505, determined the structure activity relationships and evaluated their efficacy in tissue culture models of epithelial ovarian cancer (EOC) and non-small cell lung cancer (NSCLC). These data led us to the identification of TDRL-551, which exhibited a greater than 2-fold increase in in vitro and cellular activity. TDRL-551 showed synergy with Pt in tissue culture models of EOC and in vivo efficacy, as a single agent and in combination with platinum, in a NSCLC xenograft model. These data demonstrate the utility of RPA inhibition in EOC and NSCLC and the potential in developing novel anticancer therapeutics that target RPA-DNA interactions.
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.
Повний текст джерелаKo, Eunhwa. "Exploring Key Orientations of Small Molecules to Disrupt Protein-protein Interactions." Thesis, 2012. http://hdl.handle.net/1969.1/ETD-TAMU-2012-05-10961.
Повний текст джерелаNunes, Rute Cláudia Correia Sacadura. "The therapeutic potential of small molecules p53-MDM protein-protein interaction inhibitors." Master's thesis, 2016. http://hdl.handle.net/10451/34367.
Повний текст джерелаAo longo dos anos, vários estudos científicos têm comprovado a importância da proteína supressora de tumor p53 na homeostase celular. Esta proteína encontra-se inativada em aproximadamente 50% dos tumores humanos, quer seja por mutação ou por deleção do seu gene. Por outro lado, a inativação da p53 por inibição reversível é frequentemente observada nos tumores que expressam a forma selvagem da proteína. Esta inativação pode resultar da sobre-expressão dos seus reguladores negativos, tais como a proteínas MDM2 e MDMX, conduzindo a patologias oncogénicas caracterizadas principalmente pela expressão da p53 do tipo selvagem. Vários estudos têm demonstrado que a interação da p53 com as MDM’s envolve três aminoácidos hidrofóbicos (Phe19, Trp23 e Leu26) da proteína p53. Além disso, sabe-se que a reativação da p53 é facilitada pela inibição destas interações. Nos últimos anos, várias famílias de compostos têm sido concebidas e desenvolvidas como moduladoras da atividade da p53. No entanto, o objetivo de desenvolver uma terapia anti-tumoural baseada na inibição das interações p53-MDM’s, e consequentemente na reativação da p53, encontra-se ainda no início, com apenas alguns candidatos em ensaios clínicos. Deste modo, torna-se premente a descoberta e desenvolvimento de inibidores mais potentes e seletivos para a interação entre a p53 e os seus reguladores negativos. Nos últimos anos, o nosso grupo de investigação tem vindo a investigar o potencial de várias famílias de spirooxindoles com anéis de cinco membros para o tratamento do cancro. Trabalhos anteriormente desenvolvidos pelo grupo, mostraram que as spiropirazolinas e spiroisoxazolina oxindoles apresentam propriedades anticancerígenas in vitro. O anel spiro encontrado nestes compostos funciona como uma estrutura heterocíclica rígida, a partir da qual podem ser projetados os três grupos lipofílicos que mimetizam a Phe19, Trp23 e Leu26 da p53. Estudos mais detalhados sobre o mecanismo de ação das spiroisoxazolina oxindoles mostraram que estes compostos inibem a interação p53-MDM2. No entanto, estes compostos apenas induziram moderada atividade anti-proliferativa (IC50 cerca de 35 μM) para a linha celular de cancro colo-retal humano HCT-116. Estudos de química computacional indicaram que esta moderada atividade resulta provavelmente da orientação espacial do oxindole nestes compostos não permitir que mimetizasse o resíduo Trp23 da p53, fundamental para ocorrer a ligação à proteína MDM2. Em particular, os estudos de docking molecular mostraram que o oxindole é projetado para a cavidade que seria ocupada pela Phe19 da proteína p53, enquanto os grupos aromáticos ligados ao anel de isoxazolina são projetados para as cavidades Trp23 e Leu26 da p53. A substituição do átomo de oxigénio do anel de isoxazolina por um grupo N-Ar, poderia permitir não só a inclusão de mais um substituinte no anel de 5 membros, como uma reorientação dos substituintes do anel de 5 membros de forma a ocuparem as cavidades da MDM2 a que se ligam os aminoácidos da p53. Por esse motivo, foi desenvolvida uma família de spiropirazolina oxindoles que foi testada nas linhas celulares de cancro da mama humano, MCF-7 e MDA-MB-231. Os compostos mais ativos apresentaram um valor de IC50 cerca de 7 μM. Adicionalmente, estes compostos apresentaram seletividade para a linha celular MDA-MB-231 e não foram tóxicos em células não tumorais Hek-293T. Nesta dissertação, otimizou-se esta família de compostos (spiropirazolina oxindoles) e avaliou-se em mais detalhe os seus efeitos biológicos. As spiropirazolina oxindoles foram obtidas através de uma reação de cicloadição 1,3-dipolar entre 2-indolinonas e nitrilo iminas (formadas in situ a partir de cloretos de hidrazonoílo). Esta nova biblioteca de compostos foi caracterizada e posteriormente avaliada quanto ao seu potencial anti-proliferativo in vitro, utilizando as linhas celulares humanas de cancro colo¬retal HCT-116 e cancro da mama MCF-7 e MDA-MB-231, e glioma de murino GL-261. Para a linha de cancro colo-retal os compostos apresentaram atividades entre os 11-13 µM, e para as linhas de cancro da mama MCF-7 e MDA-MB-231 apresentaram atividades de 7-12 µM e 6-11 µM, respetivamente. No caso da linha celular de glioma de murino, apenas um composto apresentou valores de atividade anti-proliferativa na mesma gama de valores com um IC50 de 19 µM. De salientar, a inclusão de um grupo N-Ar aumentou para mais do dobro a capacidade anti-proliferativa em HCT-116 p53, quando é feita uma comparação direta entre os compostos equivalentes de spiroisoxazolina oxindoles. Com o intuito de avaliar o potencial citotóxico dos compostos em células saudáveis, foi realizado o ensaio de viabilidade celular em fibroblastos de colon humano normal e em culturas primárias de astroglia de murino. Como resultado, dois compostos (2e e 2m) pertencentes à família spiropirazolina oxindoles não apresentaram citotoxicidade nas células saudáveis, apesar de serem citotóxicos nas linhas celulares de cancro. O mesmo não se verificou para o composto 2q, para o qual foi observada citotoxicidade tanto em células normais como cancerígenas. Os compostos não citotóxicos em células normais foram então avaliados quanto à sua capacidade de indução de apoptose e paragem do ciclo celular na linha celular HCT-116. Os resultados demonstraram que estes compostos induzem tanto a morte por apoptose como a paragem do ciclo celular na fase G0/G1, estando ambos os fenómenos dependentes do tempo de exposição ou concentração de composto utilizada. Com a finalidade de confirmar a capacidade desta família de compostos para induzir a morte celular, foram ainda avaliados os níveis de libertação da enzima citoplasmática lactato desidrogenase (LDH) indicativos do grau de rutura da membrana celular e, por conseguinte, de morte. Os resultados obtidos corroboraram o ensaio de apoptose, confirmando assim a capacidade de indução de morte dependente da concentração. As spiropirazolina oxindoles apresentaram ainda a capacidade de aumentar os níveis de expressão da p53 e induzir a inibição da MDM2, através da diminuição dos seus níveis de expressão proteica. Adicionalmente, a aptidão destes compostos para inibir a interação p53-MDM2 foi observada através do ensaio de complementação de fluorescência bimolecular (BiFC), e foi ainda verificada uma boa estabilidade em PBS (pH 7.4). Por último, foi observado um efeito sinergético entre um agente quimioterapêutico amplamente utilizado na clínica e um dos compostos em estudos. As spiropirazolina oxindoles foram também avaliadas quanto à capacidade de induzir apoptose e paragem do ciclo celular na linha de glioma de murino GL-261. No entanto, os resultados obtidos não demonstraram qualquer evidência de indução de apoptose ou paragem do ciclo celular nestas células, indicando que estes compostos não têm potencial terapêutico neste tipo de tumores. No âmbito desta tese foi também estudado em mais detalhe o mecanismo de ação de três spirotriazolina oxindoles previamente desenvolvidas no grupo como potenciais agentes anticancerígenos. Resultados obtidos anteriormente, tinham demonstrado que esta família apresentava boa seletividade para as linhas de cancro da mama MCF-7 e MDA-MB-231, sem apresentar citotoxicidade na linha não-tumoral Hek-293T. Observou-se ainda a capacidade destes compostos para inibir a interação p53-MDM2, ativar as caspases-3 e -7 e, consequentemente, induzir apoptose. Por último, uma boa estabilidade em plasma já tinha sido observada para os compostos em estudo. De forma a estudar o eventual mecanismo de ação desta família de compostos como potenciais agentes anticancerígenos, na presente dissertação, testaram-se os compostos mais promissores de spirotriazolina oxindoles em células da linha de cancro colo-retal HCT-116, tendo-se verificado que estes compostos induzem apoptose e clivagem da PARP, assim como a paragem do ciclo celular na fase G0/G1, sendo esta dependente do tempo de exposição ou da concentração de composto utilizada. Adicionalmente, avaliou-se a capacidade destes compostos para ativar a p53 e diminuir os níveis de expressão de MDM2, indicando uma potencial inibição da interação p53-MDM2. A indução de apoptose e paragem do ciclo celular foi também avaliada na linha celular de cancro da mama MDA-MB-231. Contudo, os resultados obtidos não demonstraram qualquer indução de apoptose após 72 horas de exposição das células ao composto. Porém, às 48 horas de exposição das células ao composto foi possível verificar a ativação das caspases-3 e -7 e paragem do ciclo celular na fase G2/M. Por último, os compostos mais promissores de spirotriazolina oxindoles foram testados em fibroblastos de colon humano normal, não se tendo verificado citotoxicidade para as concentrações testadas. Em suma, nesta dissertação demonstrou-se o potencial de cinco compostos (2e, 2m, 7f, 7h e 7z) pertencentes a duas famílias de spirooxindoles, contendo anéis heterocíclicos de 5 membros, como agentes anticancerígenos e inibidores da interação proteína-proteína p53-MDM2.
Over the years, several scientific studies have been proving the importance of the p53 tumour suppressor protein, in cellular homeostasis. This protein is found inactivated in approximately 50% of human cancers, by mutation or deletion of its gene. Moreover, the inactivation of p53 by reversible inhibition is frequently observed in various human cancers, especially in those expressing wild type p53. This inactivation results from overexpression of its negative regulators such as MDM2 and MDMX, leading to oncogenic pathologies, mostly characterized by expression of a p53 wild type form. Several studies have shown that p53 interaction with its negative regulators involves three main hydrophobic amino acids (Phe19, Trp23 and Leu26) in the p53 protein. Moreover, it is known that p53 reactivation is facilitated by inhibition of its negative regulators. In recent few years, several families of compounds were designed and developed as modulators of p53. However, the development of a p53 reactivating cancer therapy through inhibition of p53–MDM´s interaction is still at the beginning, with only a few candidates entering clinical trials. Therefore, the discovery of more powerful and selective p53–MDM´s interaction inhibitors are still an unmet need. The work developed in this master thesis aimed at developing new anticancer agents containing a spirooxindole scaffold having a pyrazoline ring. The spiro ring works as the rigid heterocyclic scaffold, from which the three lipophilic groups can be projected to mimic the p53 amino acids. The first goal included the development and optimization of a potential new anticancer agent by 1,3-dipolar cycloaddition reaction, complemented with biological activity studies, such as evaluation of cell death and cell cycle progression, and analysis of p53¬MDM2 interaction. In addition, studies of combination therapy using the newly synthetized molecules and a chemotherapeutic agent commonly used in the clinic, were also performed and finally, the stability of the compound in a saline solution was assessed. The second main goal of this thesis was to understand the effect of changing the carbon atom by a nitrogen atom in position 4´ of the pyrazoline ring. The results presented here reveal the potential anticancer activity of the new molecules, as shown by the ability to induce apoptosis and cell cycle arrest, inhibit the interaction between p53 and MDM2, while presenting good stability in PBS and no cytotoxic effects in normal human cells. Furthermore, a synergistic effect with the chemotherapeutic agent was observed. The change of the carbon atom for a nitrogen atom in position 4´ (pyrazoline ring replaced by a tryazoline ring) led to a new family of small molecules that has the ability to increase the expression of p53, thus leading to apoptosis and cell cycle arrest. In addition, these compounds were not cytotoxic in human normal cells.
Purvis, Amelia. "Using Small Molecules to Inhibit an E2A-PBX1:CBP Interaction Involved in Acute Lymphoblastic Leukemia." Thesis, 2009. http://hdl.handle.net/1974/5118.
Повний текст джерелаThesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2009-08-31 11:13:19.517
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.
Повний текст джерела國立臺灣海洋大學
生物科技研究所
95
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 systems, mannose/Con-A, haparin/A27Laa, and inhibitors/α 1,2-L-fucosidase were investigated in this study. In the first part of this thesis, the mannose/Con-A interaction will be used the assay optimization, kinetic study, and investigation of detection limit. Our result shows our nanoscale probe facilitating the fast interaction of mannose and Con A; the reaction time can be completed within 15 min with detection limit of 15 ng. For epitope mapping, the carhohydrate-binding peptides were identified with various proteases (trypsin, chymotrypsin, and Glu-C), consistent with reported binding sites by X-ray crystallization analysis. Moreover, the subtle structure change of Con-A/mannose in metal environment can be observed. For harparin/A27Laa system, the peptide at m/z 2694.6 (residue 1-32) of A27Laa was identified, which contains basic strip of 12 residues responsible for binding to cell-surface heparan sulfates. Although A27Laa lost its C-terminal, we found the epitope can be bound to the heparin-MNPs in our approach. For α1,2-L-fucosidases/inhibitor system, IV we probed the structural differences of the epitopes for three fuconojirimycin inhibitors: Inhibitor1:(2R,3S,4S,5S)-2-(aminomethyl)-6-methylpiperidine-3,4,5-triol Inhibitor2: 5-(3-aminopropoxy)-2-methylpiperidine-3,4-diol Inhibitor3:1-(3-aminopropyl)-2-methylpiperidine-3,4,5-triol and the effects of different length of linker conjugated on the surface of MNPs. The change of binding epitopes is consistent to the structure modeling of α1,2-L-fucosidase complexed with different inhibitor. Moreover, we found that the effect of digestion time is critical for the epitope mapping. Given the flexibility of nanoprobe derivation, adaptation to various proteases, and the high rapid and high sensitivity analysis, we believe our approach hold great promise in probing binding epitopes of small molecule and proteins.
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.
Повний текст джерелаShahani, 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.
Повний текст джерела