Dissertations / Theses on the topic 'Allosteric ligands'

Photopharmacology has the main purpose to allow the control of protein activity with light. The most exploited strategy used to achieve this objective is the freely diffusible photopharmacology and it is based in the use of photosensitive ligands. These ligands are small bioactive molecules, which include a part of their structure (i.e. photoswitch) that can experience molecular changes upon illumination with a determined wavelength of light. These ligands can freely diffuse and they can be applied with systems expressing native proteins. Azobenzene is the most common photoswitch used in photopharmacology and it can switch with near UV light from the flat and long trans isomer to a shorter bent cis configuration. The reverse photoisomerization can be achieved either with visible light or thermally with light. Thus, if we include azobenzene in the molecular scaffold of a ligand by means of a replacement of a particular moiety (azologization), we can obtain new azo compounds that will resemble to the original ligand, but their structural shape will dramatically changes upon illumination (photoisomerization). Therefore, the two possible isomers will have distinct binding modes to the target protein and will lead to different protein activities under different light conditions, which is known as photoswitching. Metabotropic Glutamate Receptors (mGluRs) belong to the class C/Glutamate family of G Protein-Coupled Receptors and control many neuronal and glial functions. mGlu receptors are endogenously activated by glutamate, which is the major excitatory neurotransmitter in the central nervous system (CNS), but they can also be activated or inactivated by allosteric modulators. They are usually considered better drug candidates than the orthosteric ligands because usually highly specific for a receptor and able to modulate the activity of a given receptor without blocking endogenous ligand binding. First of all, we designed and synthesized three families of compounds, using an azo-replacement strategy, to obtain photoswitchable allosteric modulators with possible NAM activity in mGlu5 in the cis isomers, while in the trans form they are inactive. This behavior is easily controlled by illuminating with different wavelengths and it is reversible in vitro. All the three families were inactive as NAMs, but some results suggest that the compounds could act as mGlu5 PAMs in trans form. Studies are continuing in this direction (Chapter 1). Next, we carry out the design and synthesis of compounds to improve PAM activity at the mGlu4 receptor and increase selectivity over the other group III mGluRs of at least one azo benzene candidate with a structure similar to Optogluram, the first photoswitchable positive allosteric modulator for the mGlu4 receptor. We obtained Optogluram-2 with good pharmacological potency and improved the photoisomerization properties. Under 380 nm light, the potency of Optogluram-2 is significantly reduced. The change in photoinduced potency observed is greater in Optogluram-2 than in Optogluram. Optogluram-2 has similar potency to Optogluram but is more selective for mGlu4 both on the receptors of the same group III as on the other mGluRs. All this indicates that Optogluram-2 can induce an improved activated/deactivated profile change as well as have an optimal selectivity for more complex assays, such as in vivo assays (Chapter 2). Additionally, we synthesized two series of compounds to find the first photoswitchable compound to selectively enable optical control of the endogenous mGlu1 receptor. Photoglurax-1 arose as a PAM of mGlu1 with micromolar potency in the trans isomer. Under 380nm light, the potency is significantly reduced. Photoglurax-1 turned out to be an equipotent mGlu4 PAM and therefore its general profile is not suitable for in vivo translation as a possible mGlu1 PAM tool compound. However, a dual mGlu1/mGlu4 PAM activity could be intriguing for an antipsychotic agent, since mGlu4 PAM activity can alleviate catalepsy, a major adverse event with standard antipsychotic drug treatment. In contrast, Photoglurax-2 acts as a mGlu1 PAM and does not show any observable allosteric effect on mGlu4 or activity on mGlu5, and therefore Photoglurax-2 represents a potential in vivo photoswitchable PAM mGlu1 tool compound. Reversible monitoring of mGlu1 activity obtained with light can be very advantageous in studying the pharmacological and physiological implications of mGlu1 in many diseases with unprecedented precision (Chapter 3). Finally, we designed and synthesized a family of novel photoswitchable azoheteroarenes as mGlu1 NAMs with an active trans isomer and an inactive cis isomer to reversibly inactivate the function of the mGlu1 receptor. The potencies of the trans configurations of some compounds of the family are in the micromolar range . Unfortunately, after 400 nm illumination the results were inconclusive due to artifacts that could originate from a possible toxicity of cis azo compounds. More experiments should be done with cells that do not express mGlu1 and also changing the light system to corroborate eventual toxicity (Chapter 4). Likewise, we use some of these compounds in their trans form, therefore without applying light, as tools to expand the knowledge about the nature of the intermediate states induced by mGlu receptor agonists in studies of fluorescence conformational dynamics. Analysis of the effect of mGlu1 NAMs on receptor conformational changes is reported in Chapter 4.
Los receptores metabotrópicos de glutamato (mGlu) son GPCRs distribuidos a través del CNS y se consideran dianas farmacológicas para trastornos neurológicos, tales como el dolor neuropático y la enfermedad de Parkison, entre otras. En primar lugar, diseñamos y sintetizamos tres familias de compuestos, utilizando una estrategia de azo- reemplazo, para obtener moduladores alostéricos de GPCR fotoconmutable con posible actividad NAM en mGlu5 en los isomeros cis, mientras que en la disposición trans son inactivos. Este comportamiento se controla fácilmente con iluminación con diferentes longitudes de onda y es reversible in vitro. Ninguna familia resultò activa como NAMs, pero algunos resultados sugieren que los compuestos podrían actuar como PAMs mGlu5 en forma trans. La investigación continúa siguiendo esta dirección (Capítulo 1). Seguidamente, realizamos el diseño y sintesis de compuestos para mejorar la actividad de PAM en el receptor mGlu4 y aumentar la selectividad sobre los otros mGluR del grupo III de al menos un candidato a azobenceno con estructura similar a Optogluram, el primer modulador alostérico positivo fotoconmutable para el receptor mGlu4. Obtuvimos Optogluram-2 con buena potencia farmacologica y mejoramos las propriedades de fotoisomerizacion. Bajo una luz de 380 nm, la potencia de Optogluram-2 se reduce significativamente. El cambio de potencia fotoinducido observado es mayor en Optogluram-2 que en Optogluram.Optogluram-2 tiene potencia parecida a Optogluram pero es màs selectivo para mGlu4 tanto sobre los receptores del mismo grupo III como sobre los demas. Todo esto indica que Optogluram-2 puede inducir un cambio de perfil activado/desactivado mejorado asì como tener una selectividad optimal para ensayos más complejos, como los ensayos in vivo (Capítulo 2). Sintetizamos dos series para encontrar el primer compuesto fotoconmutable para habilitar selectivamente el control óptico del receptor mGlu1 endógeno. Photoglurax-1 surgió como un PAM de mGlu1 con potencia micromolar en el isómero trans. Bajo una luz de 380 nm, la potencia se reduce significativamente. Photoglurax- 1 resultó ser un mGlu4 PAM equipotente y por eso su perfil general no es apropiado para una traducción in vivo como una posible herramienta molecular mGlu1 PAM. Sin embargo, una actividad dual mGlu1/mGlu4 PAM podría ser intrigante para un agente antipsicótico,ya que la actividad mGlu4 PAM puede aliviar la catalepsia, un evento adverso importante con el tratamiento estándar con fármacos antipsicóticos. En cambio, Photoglurax-2 actúa como un PAM mGlu1 y no muestra ningún efecto alostérico observable en mGlu4 ni actividad en mGlu5 y por lo tanto Photoglurax-2 representa una potencial herramienta molecular PAM mGlu1 fotoconmutable in vivo. El control reversible de la actividad de mGlu1 obtenido con luz puede ser muy ventajoso para estudiar las implicaciones farmacológicas y fisiológicas de mGlu1 en muchas enfermedades con una precisión sin precedentes (Capítulo 3). Finalmente, intentamos diseñar y sintetizar una familia de novedosos azoheteroarenos fotoconmutables como NAMs de mGlu1 con un isomero trans activo y un isomero cis inactivo para inactivar reversiblemente la función del receptor mGlu1. Las potencias de las configuraciones trans de algunos compuestos de la familia estan en el rango de micromolaridad. Desafortunadamente, tras una iluminación de 400 nm los resultados fueron no concluyentes debido a artefactos que podrían originarse a partir de una posible toxicidad de los compuestos cis azo. Se deben realizar más experimentos con células que no expresen mGlu1 y cambiando tambien el sistema de luz para comprobar si se trata de toxicidad (Capítulo 4). Asimismo, utilizamos algunos de estos compuestos en su forma trans, por lo tanto sin aplicar luz, como herramientas para ampliar el conocimiento sobre la naturaleza de los estados intermedios inducidos por agonistas de los receptores mGlu en estudios de dinámica conformacional de fluorescencia. El análisis del efecto de los NAMs de mGlu1 sobre los cambios conformacionales del receptor están reportados en el Capítulo 4. En resumen, encontramos como obtener un interruptor molecular entre varias actividades farmacologicas. Ademàs, demostramos que la fotofarmacologia presenta ventajas respecto a la farmacologia convencional, ya que permite ajustar la activacion del receptor con luz.

In the brain events happen in the scale of milliseconds, and the fine processes of neurons and neuroglia are highly compartmentalized at a microscopic level. These exclusive features of the brain define extremely precise temporal and spatial patterns of cellular activity, which are of fundamental importance for its proper functioning, because they allow the fast processing, sorting, integration, and flow of information with high reproducibility and precision. To gain deeper understanding of how these patterns are organized in time and space, we need new tools that overcome the spatiotemporal limitations of the currently available techniques. Recently, neurobiology was revolutionized by the idea of using light to control neuronal proteins remotely with millisecond- and micrometer-precision, which led to the development of a new field of study called optogenetics. After more than a decade, the control of protein function with light has gone far beyond optogenetics and its need of genetic manipulations. Optopharmacology is now gaining importance because it is less invasive and suitable for controlling endogenous proteins with light, and each year compounds with enhanced photochemical and pharmacological properties are developed. This thesis reviews the optopharmacological tools developed so far to study a family of neuronal proteins called metabotropic glutamate (mGlu) receptors. We are interested in these proteins because they participate in neurotransmission, and are link to neuropathologies when dysfunctional. Thanks to pioneering advances in probing these receptors with light, many features of mGlu signaling have been unraveled, and it is now emerging that these receptors follow activation mechanisms different from those initially foreseen. Still, it is not clear what their exact kinetics are, or which are the functional consequences of temporal and spatial patterns of activity – which are widespread both among brain structures and across evolution. Despite the fundamental relevance of mGlu receptors to brain computing in physiology and disease, the mechanisms that govern their functioning are still partially understood, and this is mainly due to the scarcity of tools to activate mGlu receptors with spatiotemporal precision. The aim of this thesis was to expand the toolbox of optical switches to activate with light mGlu receptors, with special interest in respecting the physiological context of their activation. For that purpose, we discarded approaches based on genetic engineering of receptors, as well as irreversible uncaging of compounds. We preferred the use of optopharmacology, and specifically applied it to allosteric modulators, which display higher selectivity and more physiological activation than orthosteric ligands. This objective implied technical challenges due to the structural restrictions of mGlu allosteric binding pockets, but at the same time offered high gains to spatiotemporally control these receptors both in therapeutic and basic research applications. From these premises, we: 1. developed the first light-regulated allosteric modulators targeting metabotropic glutamate receptors. The molecular design, in vitro and in vivo characterization of alloswitch-1 and G4optoNAM are presented in Chapters 1-2. 2. expanded the knowledge about this new class of compounds through a library of compounds derived from alloswitch-1, and present the inferred data about structure-activity relationship and optimal optopharmacological characteristics for allosteric photoswitches of mGlu receptors (Chapter 3). 3. demonstrated the functional photoisomerization of alloswitch-1 by using two-photon stimulation, with the aim of exploring the resolution limits of reversible optical switches (Chapter 4). Overall, this thesis shows for the first time the design and characterization of optical switches for the allosteric and remote control of endogenous mGlu receptors in vitro and in vivo with light. This advance broadens the availability of optical tools in research to manipulate mGlu receptors with high temporal and spatial resolution, and represents a step forward in innovative opportunities to treat neuropathologies with light.
En el sistema nerviós els esdeveniments es desenvolupen en l’escala temporal dels milisegons, i els processos que tenen lloc en neurones i cèl·lules de la glia presenten compartimentalitzacions microscòpiques. Aquesta organització determina uns patrons d’activitat ben definits temporal i espacialment, els quals permeten el precís funcionament del sistema nerviós per tal de transmetre, integrar i processar la informació d’una forma rapida i especifica. Per entendre millor el modus operandi del cervell en el temps i l’espai, calen noves eines que permetin superar les limitacions espaitemporals de les tecnologies existents per l’observació passiva o l’activa manipulació del sistema nerviós. Una de les estratègies més rapides i precises per activar e inactivar proteïnes neuronals es basa en la seva fotosensibilització, per tal de poder-les controlar mitjançant la precisió espai-temporal incomparable que la llum ofereix. Aquesta tesi fa un resum de les eines òptiques disponibles per detectar (sensors) e induir (commutadors) l’activitat d’una família de proteïnes neuronals denominades receptors metabotropics de glutamat (mGlu). Estem interessats en aquests receptors per la importància que tenen com moduladors de la neurotransmissió, i el seu rol en el desenvolupament de neuropatologies. L’objectius de la tesi fou desenvolupar eines optofarmacològiques pel control òptic i reversible dels receptors mGlu amb llum, considerant els grans avantatges d’especificitat espaitemporal que ofereix el fotocontrol de proteïnes i l’escassetat de tals eines. El primer capítol descriu el disseny, la síntesi i la caracterització d’alloswitch-1, el primer fotocommutador al·lostèric capaç d’activar receptors mGlu amb llum de forma reversible. El segon capítol il·lustra la caracterització de G4optoNAM, un fotocommutador al·lostèric actiu en receptors mGlu4. El tercer capítol recull una llibreria de compostos derivats del precursor alloswitch-1 amb diverses substitucions químiques, que presenten característiques fotofísiques i optofarmacològiques variades. Al quart i últim capítol demostrem la capacitat dels alloswitches de fotoisomeritzar amb il·luminació micromètrica amb un làser multifotó. La nostra capacitat d’expandir el ventall d’eines optofarmacològiques que permeten un control farmacològic de receptors neuronals amb llum, de forma remota i no invasiva, ha aportat a la comunitat científica noves metodologies farmacològiques per a l’estudi de la fisiopatologia del sistema nerviós.

Le récepteur du glucagon-like peptide-1 (GLP-1) (GLP-1R) est un récepteur couplé aux protéines G de classe B et une cible médicamenteuse importante dans le traitement du diabète de type 2 (DT2)
The glucagon-like peptide-1 (GLP-1) receptor (GLP-1R) is a class B G protein-coupled receptor and an important drug target in the treatment of type 2 diabetes (T2D)

Molecular recognition, defined as the specific interactions between two or more molecules, is at the center of many biological processes including catalysis, signal transduction, gene regulation and allostery. Allosteric regulation is the modification of function caused by an intermolecular interaction. Allosteric proteins modify their activity in response to a biological signal that is often transmitted through the interaction with a small effector molecule. Therefore, determination of the origins of intermolecular interactions involved in molecular recognition and allostery are essential for understanding biological processes. Classically, molecular recognition and allosteric regulation have been associated to structural changes of the system. NMR spectroscopic methods have indicated that changes in protein dynamics may also contribute to molecular recognition and allostery. This thesis is an investigation of the contributions of both structure and dynamics in molecular binding phenomena. In chapter I, I describe molecular recognition, allostery and examples of allostery and cooperativity. Then I discuss the contribution of protein dynamics to function with a special focus on allosteric regulation. Lastly I introduce the hemoglobin homodimer, HbI of Scapharca inaequivalvis and the mRNA binding protein TIS11d. Chapter II is the primary focus of this thesis on the contribution of protein dynamics to allostery in the dimeric hemoglobin of scapharca inaequivalvis, HbI. Thereafter I concentrate on the mechanism of adenine recognition of the Tristetraprolin-like (TTP) protein TIS11d; this study is detailed in Chapter III. In Chapter IV I discuss broader impacts and future directions of my research. This thesis presents an example of the use of protein NMR spectroscopy to probe ligand binding. The studies presented in this thesis emphasize the importance of dynamics in understanding protein function. Measurements of protein motions will be an element of future studies to understand protein function in health and disease.

The Trk family of tyrosine kinase receptors and the common p75NTR receptor are neurotrophin receptors. Nerve growth factor (NGF) binds TrkA, brain-derived neurotrophic factor (BDNF) binds TrkB, and neurotrophin-3 (NT-3) binds TrkC. The extracellular domain of the Trk receptor has five subdomains: a leucine-rich motif (D2), two cysteine-rich motifs (D1, D3) and immunoglobulin-like subdomains Ig-C1 (D4) and Ig-C2(D5). The Trk D4 subdomain regulates ligand-independent activation. The TrkA-D5 and TrkB-D5 subdomains regulate cognate ligand binding and Trk activation. However, the p75NTR receptor binds all neurotrophins and regulates ligand affinity and Trk signals. We showed that p75NTR affects Trk ligand - binding and activation of Trks by changing Trk subdomain utilization. When p75NTR is coexpressed, NGF can activate TrkA via the cysteine-1 subdomain (D1), and BDNF can activate TrkB via leucine-rich motif (D2) and cysteine-2 (D3) subdomains. We hypothesized conformational or allosteric regulatory mechanisms. To further study the interactions between ligands and Trks, we examined TrkA binding to NT-3 as a heterologous ligand because these interactions are biologically relevant. We found the TrkA “hot spot” functional docking sites used by NT-3. We demonstrate that TrkA-D5 has partially overlapping but distinct binding and activation “hot spots” for both, NGF and NT-3. Moreover, ligand - binding studies have identified additional NT-3 binding/allosteric site on TrkA-D4. NT-3 binding to both sites induces full agonism. Conversely, the TrkA-D5 NT-3 binding site is partially agonistic, but antagonizes NGF activity. Lasly, we address NT-3 binding and activation sites on the TrkC receptor by raising a monoclonal antibody that recognizes the juxtamembrane-linker domain of the TrkC receptor. This antibody is an artificial TrkC receptor agonist. The epitope of mAb 2B7 defines a previously unknown hot spot of TrkC. Binding to this “hot spot” induces survival but n
La famille de récepteurs de Trk tyrosine kinase et le récepteur p75NTR sont des récepteurs de neurotrophines. Le facteur de croissance nerveuse (NGF) intéragit avec le récepteur TrkA, le facteur neurotrophique dérivé du cerveau (BDNF) intéragit avec le récepteur TrkB et la neurotrophine-3 (NT-3) intéragit avec TrkC. Le domaine extracellulaire du récepteur Trk contient cinq sous-domaines: un motif riche en leucine (D2), deux motifs riches en cysteine (D1, D3) et des sous-domaines de type immunoglobuline Ig-C1(D4) et Ig-C2(D5). Le sous-domaine Trk D4 régule l'activation indépendante de ligand. Les sous-domaines TrkA-D5 et TrkB-D5 régulent la liaison de ligands endogènes ainsi que l'activation du récepteur Trk. Le récepteur p75NTR intéragit avec toutes les neurotrophines et régule l'affinité des ligands et les signaux issues de l'activation du récepteur Trk. Par ailleurs, nous avons démontré que le p75NTR affecte la liaison du ligand au récepteur Trk en changeant l'activation de l'utilisation des sous-domaines. Lorsque le recepteur de p75NTR est coexprimé, le NGF peut activer le récepteur TrkA via le sous-domaine cysteine-1 (D1) et BDNF peut activer TrkB via le motif riche en leucine (D2) ainsi que via le sous-domaine cysteine-2 (D3). Nous avons examiné la liaison d'un ligand hétérologue, NT-3 sur le récepteur TrkA afin d'étudier plus profondément les interactions entre les ligands et le récepteur TrkA. Ces interactions sont biologiquement pertinentes. Pour faire ceci, nous avons tout d'abord identifié les « points chauds » présents sur le récepteur TrkA qui servent des sites d'amarrage fonctionnels du ligand NT-3. Nous avons démontré que le sous domaine TrkA-D5 possède deux points chauds distincts, notamment un point chaud qui sert comme le site d'amarrage et d'activation du NGF et un point chaud qui sert comme le site d'amarrage et d'activation de la NT-3. Toutefois, ces deux sites d'amarrage se chevauchent partiellement. D

Downstream regulatory antagonist modulator (DREAM) is a calcium sensing protein that co-assembles with KV4 potassium channels to regulate ion currents as well as with DNA in the nucleus, where it regulates gene expression. The interaction of DREAM with A-type KV4 channels and DNA has been shown to regulate neuronal signaling, pain sensing, and memory retention. The role of DREAM in modulation of pain, onset of Alzheimer’s disease, and cardiac pacemaking has set this protein as a novel therapeutic target. Moreover, previous results have shown a Ca2+ dependent interaction between DREAM and KV4/DNA involving surface contacts at the N-terminus of DREAM. However, the mechanisms by which Ca2+ binding at the C-terminus of DREAM induces structural changes at the C- and N-terminus remain unknown. Here, we present the use of biophysics and biochemistry techniques in order to map the interactions of DREAM and numerous small synthetic ligands as well as KV channels. We further demonstrate that a highly conserved network of aromatic residues spanning the C- and N-terminus domains control protein dynamics and the pathways of signal transduction on DREAM. Using molecular dynamics simulations, site directed mutagenesis, and fluorescence spectroscopy we provide strong evidence in support of a highly dynamic mechanism of signal transduction and regulation. A set of aromatic amino acids including Trp169, Phe171, Tyr174, Phe218, Phe235, Phe219, and Phe252 are identified to form a dynamic network involved in propagation of Ca2+ induced structural changes. These amino acids form a hydrophobic network connecting the N- and C-terminus domains of DREAM and are well conserved in other neuronal calcium sensors. In addition, we show evidence in support of a mechanism in which Ca2+ signals are propagated towards the N-terminus and ultimately lead to the rearrangement of the inactive EF-hand 1. The observed structural motions provide a novel mechanism involved in control of the calcium dependent KV4 and DNA binding. Altogether, we provide the first mechanism of intramolecular and intermolecular signal transduction in a Ca2+ binding protein of the neuronal calcium sensor family.

Protein-ligand and protein-protein interactions are critical to cellular function. Most cellular metabolic and signal tranduction pathways are influenced by these interactions, consequently molecular level understanding of these associations is an important area of biochemical research. We have examined the thermodynamics of several protein-protein associations and the protein-ligand interactions that mediate them. Using Fluorescence Correlation Spectroscopy, we have examined the putative interaction between pig heart malate dehydrogenase (MDH) and citrate synthase (CTS). We demonstrate a specific, low-affinity interaction between these enzymes. The association is highly polyethylene glycol (PEG)-dependent, and at high concentrations of NaCl or PEG, non-specific aggregates are formed. We demonstrate that oxaloacetate, the intermediate common to both CTS and MDH, induces the association at concentrations below the Km of CTS, suggesting that the open conformation of CTS is involved in the association. Using several biophysical techniques, we have examined the subunit associations of B. stearothermophilus phosphofructokinase (PFK). We demonstrate that the inhibitor bound conformation of the enzyme has reduced subunit affinity. The kinetics and thermodynamics of the phosphoenolpyrvuate (PEP)-induced dissociation of PFK have been quantified. Binding substrate, fructose-6-phosphate (F6P), stabilizes the enzyme to inhibitor-induced dissociation by 132-fold. These data suggest that subunit associations may play a role in the allosteric inhibition of PFK by PEP. The thermodynamics of the protein-ligand associations and allosteric inhibition of E. coli phosphofructokinase have been examined using intrinsic fluorescence and hydrostatic pressure. Both ligand-binding affinity and PEP inhibition are diminished by pressure, whereas substrate-binding affinity for inhibitor-bound enzyme is pressure-insensitive. Larger entropic than enthalpic changes with pressure lead to the overall reduction in free energies. Using a fluorescence-based assay, we have developed a series of baroresistant buffer mixtures. By combining a buffer with acid dissociation of negative volume with a buffer of positive volume, a pressure-resistant mixture is produced. Alteration of the molar ratio of the two component buffers yields mixtures that are pressure-insensitive at pH values around neutrality.

Les récepteurs pentamériques canaux (pLGICs) sont des récepteurs neuronaux impliqués dans la neurotransmission rapide et qui comprennent les récepteurs suivants : nAchR, GABAR, GlyR or 5HT3R. Lorsqu’ils ne fonctionnent pas correctement ils sont impliqués dans des pathologies comme Alzheimer ou Parkinson. Dans cette étude, nous avons réalisé des simulations de dynamique moléculaire d’un homologue procaryote des pLGICs. Grâce à l’analyse de 2.5 us de simulation nous avons pu capturer la fermeture complète dudit récepteur et décrire un mécanisme de gating. Ce mécanisme en deux étapes, 1) twisting puis 2) blooming semble compatible avec tous les pLGICs. Dans un second temps, nous avons utilisé notre connaissance du mécanisme de gating afin de faire des calculs d’énergie libre le long du twisting, pour différents complexes protéine/ligands. De cette façon, nous avons pu discriminer entre des ligands actifs et inactifs et ainsi fournir des pistes pour le design de nouveaux traitements
Pentameric ligand gated ion channels (pLGICs) are brain receptors involved in fast neurotransmission and include nAchR, GABAR, GlyR or 5HT3R. When dysfunctioning, they are involved in diseases such as Alzheimer’s and Parkinson’s. In this study we have performed molecular dynamic simulations of an eukaryotic homologue of the pLGICs (GluCl) to understand the gating mechanism of pLGICs. Thanks to the analysis of two 2.5 us long simulations in which we could capture the full closing of the receptor we described in great details a gating mechanism in two steps, first twisting then blooming, that we believe applicable to the whole pLGICs family. In a second time we used our description of the gating mechanism to perform free energy calculations along the twisting reaction coordinate, for various ligands in complex with GluCl. Doing so we could show a significant difference between IVM-bound and non-bound states and provide hints for the design of new treatments

Allosteric modulation of neuronal nicotinic acetylcholine receptors (nAChRs) is considered to be one of the most promising approaches for therapeutics. By binding to a site of the receptor distinct from the neurotransmitter binding site, allosteric modulators alter the response of the receptors to their agonists. There are two major locations of allosteric modulator binding sites. One is in subunit interfaces of the extracellular N-terminal domain. The other is in the transmembrane domain close to the channel gating machinery. This thesis focuses on a positive allosteric modulator of the human α4β2 nAChR, desformylflustrabromine (dFBr), which was found to exert its potentiating effects on this receptor by binding to a site in the transmembrane region of the α4 subunit. α4β2 nAChRs are the most abundant nAChR type in the brain, where they modulate a range of brain functions such as mood, cognition, nociception and reward. This receptor subtype has been shown to be sufficient and necessary for the rewarding and reinforcing properties of nicotine. In addition, α4β2 nAChRs have been implicated in aging-related cognitive dysfunction, Alzheimer’s and Parkinson’s diseases, mood disorders and a rare type of family epilepsy. dFBr is a positive allosteric modulator of the α4β2 and α2β2 nAChRs that displays selectivity against all other nAChRs. Using functional mutagenesis and structural modelling, the molecular basis for the selective potentiation of α4β2 nAChRs has been identified. The potentiating binding site of dFBr is located in the top-half of a transmembrane cavity between the M3 and M4 helices of the α4 subunit. α4Y309, α4F312 and α4L617 influence dFBr potentiation in accord with a role in dFBr binding. Alanine substitutions of these residues annulled dFBr potentiation and experiments using MTSET showed that the residues in this putative site are accessible to MTSET and that dFBr competes with MTSET for the access to the cavity. These residues map to a highly conserved intra-subunit cavity in the pentameric ligand gated ion channel (pLGIC) family. In addition, the effector system for the potentiating effects of dFBr was also identified. The post-M4 region (C-terminal) and the Cys loop residues F167 and F170 of the α4 subunit play central roles in transducing dFBr binding to potentiation of the ACh responses of the α4β2 nAChR. Whilst the residues that contribute to the dFBr binding site in the α4 are conserved across all nAChR subunits, except for α7, the post-M4 region is not. It is this region that determines the selective potentiating effects of dFBr on α4β2 nAChR. This finding, together with recent data on the effect of propofol in bacterial and invertebrate evolutionary related pLGICs, suggest that for highly conserved transmembrane domain allosteric binding sites, the effector machinery associated with these sites, rather than the binding sites, define the receptor selectivity of the modulators.

Chemistry
Ph.D.
Protein-ligand binding and protein allostery play a crucial role in cell signaling, cell regulation, and modern drug discovery. In recent years, experimental studies of protein structures including crystallography, NMR, and Cryo-EM are widely used to investigate the functional and inhibitory properties of a protein. On the one hand, structural classification and feature identification of the structures of protein kinases, HIV proteins, and other extensively studied proteins would have an increasingly important role in depicting the general figures of the conformational landscape of those proteins. On the other hand, free energy calculations which include the conformational and binding free energy calculation, which provides the thermodynamics basis of protein allostery and inhibitor binding, have proven its ability to guide new inhibitor discovery and protein functional studies. In this dissertation, I have used multiple different analysis and free energy methods to understand the significance of the conformational and binding free energy landscapes of protein kinases and other disease-related proteins and developed a novel alchemical-based free energy method, restrain free energy release (R-FEP-R) to overcome the difficulties in choosing appropriate collective variables and pathways in conformational free energy methods like umbrella sampling and metadynamics.
Temple University--Theses

Protein ubiquitination is a key regulator of both protein stability and activity, and is involved in the regulation of a vast variety of cellular pathways. The ubiquitination system therefore provides an exciting target for drug development aiming to regulate the function of specific proteins. Our understanding of ubiquitin signalling is far from complete; and if we are to exploit this system for the benefit of human health, it is important to gain a better understanding of this complex posttranslational modification system as well as the effect of ubiquitination on the target protein. The E3 ligases MDM2 and CHIP were implicated in the control of the two transcriptional activators (TAs) IRF-1 and p53, that normally function to maintain health at the cellular and organismal level. Research carried out as part of my PhD has focused on gaining a mechanistic understanding of the ubiquitination process in particular the relationship between the E3 ligase and its substrate. Broadly, the mechanisms of E3 ligase regulation have been linked to substrate specificity and then to the physiological outcome of site-specific ubiquitination of the DNA binding domain of the TAs IRF-1 and p53. More specifically I have; (i) identified a mechanism by which the E3 ligase activity of the CHIP U-box can be allosterically regulated by ligand binding to its TPR domain. (ii) Residues on IRF-1 that are targeted by MDM2 and CHIP have been mapped, revealing that both ligases modify sites exclusively in IRF-1's DNA binding domain (DBD). Furthermore, I showed that, in its DNA bound conformation, IRF-1 is neither bound nor ubiquitinated by the ligases, suggesting a mechanism by which IRF-1 ubiquitination and possibly degradation can be regulated through its DNA binding state. And lastly, (iii) I have shown that both IRF-1 and p53, which have ubiquitin acceptor lysines in their DBD, bind DNA more stably when ubiquitinated. Modelling suggests that interactions between a positively charged surface area of ubiquitin and the negatively charged DNA can stabilises the TA-ubiquitin complex. DBD ubiquitination sites are required for full transactivation potential of both TAs, supporting a role of ubiquitin in their activation. p53 is ubiquitinated in response to activation by IR or Nutlin-3 and these ubiquitinated forms of p53 are localised in the cell nucleus associated with chromatin and do not lead to protein degradation. Taken together, the data imply that p53 and IRF-1 DNA binding ability, and thereby activity, can be modulated by ubiquitin modification.

Human glutathione synthetase (hGS) is a homodimeric enzymes that catalyzes the second step in the biological synthesis of glutathione, a critical cellular antioxidant. The enzyme exhibits negative cooperativity towards the γ-glutamylcysteine (γ-GC) substrate. In this type of allosteric regulation, the binding of γ-GC at one active site significantly reduces substrate affinity at a second active site over 40 Å away. The presented work explores protein-protein interactions, substrate binding, and allosteric communication through investigation of three regions of hGS: the dimer interface, the S-loop, and the E-loop. Strong electrostatic interactions across the dimer interface of hGS maintain the appropriate tertiary and quaternary enzymatic structure needed for activity. The S-loop and E-loop of hGS form walls of the active site near γ-GC, with some residues serving to bind and position the negatively cooperative substrate. These strong interactions in the active site serve as a trigger for allosteric communication, which then passes through hydrophobic interactions at the interface. A comprehensive computational and experimental approach relates hGS structure with activity and regulation. ATP-grasp enzymes, including hGS, utilize ATP in the nucleophilic attack of a carboxylic acid in a reaction thought to proceed through the formation of an acylphosphate intermediate. Small metal cations are known to chelate the terminal phosphates of actives site ATP, yet the role of these atoms remains unclear. In the presented work, a computational metal substitution study establishes the role these divalent cations in the catalysis of peptide bonds. The simple model is used to determine the impact of metal cations on the thermodynamics and kinetics, an important stepping stone in understanding the importance of metal cations in larger biological systems.

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 ligand-associated structural changes in GR drug discovery campaigns. The flexibility of the GR active site is such that it is capable of accommodating ligands with very different structures. Though these ligands may bind to the same pocket, they may associate with quite dissimilar conformations where some are more favorable for complexation than others. Knowledge of these changes is invaluable in guiding drug discovery efforts, indicating which compounds selectively associate with more favorable conformations and are therefore better suited for optimization and providing starting structures to guide structure-based drug design optimization efforts. In this study, we develop a mutant GR possessing a genetically encoded non-natural fluorescent amino acid in a region remote from the active site whose movement has been previously observed to correlate with active site changes. With this mutant GR, we observe a differential fluorescence pattern upon binding of two structurally distinct competitive inhibitors known to associate with unique GR conformations – one to a favorable conformation with a smaller, less solvated active site and the other to an unfavorable conformation with a larger, more solvated active site. A concomitant computational study ascribes the source of this differential fluorescence pattern to ligand-associated conformational changes resulting in changes to the local environment of the fluorescent residue. Therefore, this mutant permits the elucidation of valuable structural information with relative ease by simply monitoring the fluorescence pattern resulting from ligand binding, which indicates whether the ligand has bound to a favorable or unfavorable conformation and offers insight into the general structure of this conformation.

Glucokinase (GK) is an enzyme that catalyzes the ATP-dependent phosphorylation of glucose to form glucose-6-phosphate, and it is a tightly regulated checkpoint in glucose homeostasis. The monomeric enzyme possesses a highly exotic kinetic profile, with a sigmoidal dependence on glucose, which has been the source of vigorous investigation and debate in the last several decades. This unique regulatory behavior can be thought of as a remarkable glucose sensor, which may result in hyperglycemia when it is not active enough and hypoglycemia when it is too active. This interdisciplinary study, which draws on small angle X-ray scattering (SAXS) integrated with atomistic molecular dynamics simulations and experimental glucose binding thermodynamics, I reveal the critical regulation of the glucose sensor is due to a solvent controlled switch. Moreover, this solvent controlled switch manifests a regulatory mechanism of GK; a specific local conformational change that leads to an enzyme structure that has a much more favorable solvation energy than most of the protein ensemble. These findings have direct implications for the design of small molecule GK activators as anti- diabetes therapeutics as well as for understanding how proteins can be designed to have built-in regulatory functions via solvation energy dynamics.

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 incompatible with these non-traditional targets. We hypothesized that an integrative virtual screening campaign comprised of docking followed by refinement of best receptor–ligand complexes would effectively identify small-molecule ligands of challenging receptors. We targeted the single-stranded DNA (ssDNA) binding groove of the human RAD52, and a cryptic allosteric pocket of the Helicobacter pylori Glutamate Racemase (GR). In this project, we first determined which docking method was more appropriate for each studied non-traditional target, and then examined how good our two-step docking workflow was in finding novel active ligand scaffolds. This research developed a powerful layered virtual screening workflow for the discovery of lead compounds against challenging protein targets. Furthermore, we successfully applied a statistical analysis method, which used receiver operating characteristic (ROC) curves, to validate the selected docking protocol that would be used in the screening campaigns. Using the validated workflow, we identified a natural compound that competes with ssDNA to bind to RAD52. The performed screening campaigns also provided new insights into the studied binding pockets, as well as structure-activity relationships (SAR) and binding determinants of the ligands. Our achievements reinforce the power of the ROC curve analysis approach in directing the search for the most appropriate docking protocol and helping to speed up drug discovery in pharmaceutical research.

Els mètodes de descobriment de nous fàrmacs han evolucionat recentment gràcies a la resolució de les estructures proteiques que actuen com a dianes terapèutiques responsables de malalties o desregulacions biològiques. Aquestes estructures proteiques tridimensionals, juntament amb el desenvolupament de noves tècniques computacionals permeten el desenvolupament accelerat de nous compostos candidats a esdevenir fàrmacs. El present treball s’inicia proposant un nou mètode que millora l’elecció de compostos candidats a ser inhibidors d’una “diana difícil”, però ben coneguda com és el receptor VEGFR-2, a partir de la seva estructura tridimensional cristal·litzada, així com de compostos inhibidors coneguts de l’esmentada diana. La resolució tridimensional de l’estructura CXCR4 mitjançant cristal•lografia de raigs X a l’any 2010, ha esdevingut un avenç important a l’hora de millorar el disseny de compostos inhibidors del VIH, així com compostos antitumorals, malalties en les que intervé de forma determinant el receptor CXCR4. Així doncs, els models de cribratge virtual desenvolupats abans del 2010 dins el laboratori de disseny molecular de l’IQS (GEM) han estat generats a partir de models creats per homologia vers a altres proteïnes GPCRs i/o s’han basat solament en la forma de lligands coneguts. D’aquesta forma, a partir de les diferents estructures proteiques publicades de CXCR4, s’ha avaluat quina d’aquestes estructures presenta la conformació que distingeix millor els compostos antagonistes actius dels compostos inactius. A més, s’han avaluat múltiples mètodes de cribratge virtual de CXCR4 basats en l’estructura, en la forma del lligand i mitjançant models farmacofòrics. Una vegada obtinguda la millor estructura de CXCR4 i els millors mètodes de cribratge virtual retrospectiu, es realitzen cribratges virtuals prospectius d’una nova quimioteca generada de forma combinatòria, basada en estructures anàlogues prèviament desenvolupades al laboratori de disseny molecular de l’IQS. Addicionalment, s’ha estudiat el comportament al·lostèric del receptor CXCR4 davant de moduladors antagonistes petits i moduladors al·lostèrics agonistes de naturalesa pèptica. CXCR4 és qualificada com a una “diana difícil” per la gran mida del seu lloc actiu ortostèric, així com per l’ampli número de funcions reguladores en les que intervé el receptor. Per això la modulació al·lostèrica en CXCR4 s’ha estudiat utilitzant diferents aproximacions com són el docking cec, docking proteïna-proteïna, docking per subllocs d’unió i dinàmica molecular.
Los métodos de descubrimiento de nuevos fármacos han evolucionado recientemente gracias a la resolución de las estructuras proteicas las cuales actúan como dianas terapéuticas responsables de enfermedades o desregulaciones biológicas. Estas estructuras proteicas tridimensionales, conjuntamente con el desarrollo de nuevas técnicas computacionales están permitiendo el desarrollo acelerado de nuevos compuestos candidatos a convertirse en fármacos. El presente trabajo se inicia proponiendo un nuevo método que permita mejorar la elección de compuestos candidatos a ser inhibidores de una “diana difícil” aunque bien conocida, como es el receptor VEGFR-2, partiendo de su estructura tridimensional cristalizada y de compuestos inhibidores conocidos de dicha diana. La resolución tridimensional de la estructura del receptor CXCR4 mediante cristalografía de rayos X, en el año 2010, ha supuesto un avance importante de cara a mejorar el diseño de compuestos inhibidores del VIH, así como de compuestos antitumorales, enfermedades en las que interviene de forma determinante el receptor CXCR4. Así pues, los modelos de cribado virtual desarrollados anteriormente al 2010 en el laboratorio de diseño molecular del IQS (GEM) han sido generados a partir de modelos creados por homología a otras proteínas GPCRs y/o basados únicamente en la forma de ligandos conocidos. De este modo, partiendo de las diferentes estructuras proteicas publicadas de CXCR4, se ha evaluado cuál de dichas estructuras presenta la conformación que distingue mejor los compuestos antagonistas activos de compuestos inactivos. Además, se han evaluado múltiples métodos de cribado virtual de CXCR4 basados en la estructura, en la forma del ligando y mediante modelos farmacofóricos. Una vez obtenida la mejor estructura de CXCR4 y los mejores métodos de cribado virtual retrospectivo, se realizan cribados virtuales prospectivos de una nueva quimioteca generada combinatoriamente, basada en análogos de estructuras previamente desarrolladas en el laboratorio de diseño molecular del IQS. Adicionalmente se ha estudiado el comportamiento alostérico del receptor CXCR4 frente a moduladores antagonistas de pequeño tamaño y moduladores alostéricos agonistas de naturaleza peptídica. CXCR4 se califica como “diana difícil” debido al gran tamaño del sitio activo ortostérico, juntamente con el amplio número de funciones reguladoras en las que interviene el receptor CXCR4. Por ello la modulación alostérica en CXCR4 se ha estudiado utilizando diferentes aproximaciones, como son: docking ciego, docking proteína-proteína, docking por subsitios y dinámica molecular.
: Drug discovery methods have recently emerged thanks to the resolution of protein structures which act as therapeutic targets responsible for diseases or biological deregulations. These three dimensional structures in combination with the development of new computational techniques are accelerating the development of new candidates to become drug compounds. This work starts with the proposal of a new method that improves the selection of candidates to become inhibitors of a well-known “difficult target” such us VEGFR-2 receptor. This method is based on the crystal structure of the receptor and also by a number of inhibitors known for this target. CXCR4 crystal structure was solved in 2010 by X-ray crystallography and this has been an important event in order to improve the molecular design of HIV inhibitors, as well as anticancer compounds, diseases where CXCR4 receptor is involved. Therefore, virtual screening models developed in the laboratory of molecular design of IQS (GEM) were generated using homology models from other GPCRs and/or based on ligand shape techniques. In this sense, taking into consideration all published CXCR4 crystal structures, it has been evaluated which of them shows the most suitable conformation to distinguish antagonists actives from inactives. Moreover, different virtual screening methods have also been evaluated such us structure based methods, ligand based methods and pharmacophoric models. Once obtained the most suitable structure and the best retrospective virtual screening methods, a prospective virtual screening has been carried out using a new combinatorial library of chemical structures. This new library is based on analogous structures previously generated in the laboratory of molecular design of IQS (GEM). In addition, the allosteric behaviour of CXCR4 receptor has been studied versus small antagonist modulators and versus peptidomimetic agonist modulators. CXCR4 is classified as a “difficult target” due to the large size of its extracellular pocket that the orthosteric binding site is placed as well as the diverse number of biochemical regulations where the receptor mediates. Thus, the allosteric modulation of CXCR4 has been studied using different approaches such as blind docking, protein-protein docking, docking by subsites and molecular dynamics.

Les récepteurs canaux pentamériques (RCPs) sont des protéines membranaires présentes à la fois chez les eucaryotes comme les récepteurs à la glycine GlyR, et à la sérotonine 5-HT3R et chez certains procaryotes comme GLIC. Chez l’Homme, ces récepteurs sont impliqués dans la transmission synaptique rapide, ils sont une cible thérapeutique importante par exemple pour les anesthésiques généraux ou les anxiolytiques, et leur mutation entraine des pathologies sévères telles que des myasthénies, des épilepsies ou des maladies neurologiques rares comme l’hyperekplexie. La liaison de l’agoniste sur ces récepteurs favorise des réorganisations structurales qui amènent à un état actif pour lequel le canal est ouvert et permet le passage d’ions. Les propriétés structurales et fonctionnelles de ces récepteurs ont été étudiées et combinées dans ce travail pour explorer la dynamique conformationnelle des RCPs. Plusieurs approches par fluorescence ont été utilisées pour : 1) déterminer la cinétique de pré-activation de GLIC qui se passe à l’échelle de la centaine de microsecondes, 2) mesurer l’effet de mutations sur GLIC qui impactent profondément les réorganisations globales ce qui démontre l’importance du couplage allostérique des différentes régions de la protéine pour permettre son activation, 3) caractériser des états intermédiaires des RCPs eucaryotes qui se trouvent en amont de l’activation. Combiné à l’analyse structurale, les données de fluorescence obtenues permettent de détailler des intermédiaires conformationnels de l’activation des RCPs et d’approfondir les connaissances sur les mécanismes moléculaires qui régissent le fonctionnement normal et pathologique de ces récepteurs
Pentameric ligand-gated ion channels (pLGICs) are membrane proteins found in both eukaryotes such as the glycine and serotonin receptors and in some prokaryotes like GLIC. In Humans, these receptors are involved in fast synaptic transmission and are a major therapeutic target for general anesthetics or anxiolytics and their mutation lead to severe diseases such as myasthenia, epilepsies or rare neurological diseases like hyperekplexia. Agonist binding on these receptors promote structural reorganizations leading to the active state with an open pore allowing ion flux. Structural and functional properties of these receptors have been studied and combined in this work to explore conformational dynamics of pLGICs. Several approaches have been used to: 1) determine pre-activation kinetics of GLIC at the hundreds of milliseconds timescale, 2) measure the effect of mutations deeply impacting global reorganizations highlighting the major role of allosteric coupling of different protein domains to permit its activation, 3) characterize intermediate states of eukaryotic pLGICs upstream activation. Combined to structural analysis, fluorescence data obtained provide detailed description of conformational intermediates of pLGICs activation and deepen the knowledge of molecular mechanisms determining normal and pathological functioning of these receptors

L'acide rétinoïque (AR) joue un rôle important dans plusieurs processus cellulaires à travers la régulation de la différentiation cellulaire, de la prolifération et de l'apoptose. Ces propriétés sont à la base de l'utilisation de l'AR dans le traitement de plusieurs cancers dont la leucémie aiguë promyélocytaire. Décrypter comment l'AR contrôle l'expression de gènes spécifiques est un défi permanent pour l'étude des cancers. Les effets de l'AR sont médiés in vivo principalement par les récepteurs à l'acide rétinoïque (RARs). Il a été récemment démontré que la phosphorylation des RARs par différentes kinases est une étape nécessaire dans la régulation de leurs fonctions. Dans ce contexte, ma thèse a porté sur l’étude des mécanismes moléculaires de la régulation par phosphorylation des RARs. Nous nous sommes intéressés en particulier à deux aspects : l’effet de la phosphorylation sur le domaine de liaison au ligand (LBD) et sur le domaine N-terminal (NTD). Dans le cas du LBD, la phosphorylation induit la fixation de la Cycline H qui est une sous-unité du facteur de transcription TFIIH, alors que la phosphorylation du NTD induit une diminution d’affinité de liaison à la Vinexine beta qui est un co-répresseur. Nous avons étudié les effets de la phosphorylation par des simulations de dynamique moléculaire. Cette technique permet de caractériser la dynamique structurale et de quantifier les interactions qui stabilisent les états phosphorylés et non phosphorylés. Ce projet a permis de définir les bases moléculaires de la communication entre le RA et les cascades de phosphorylation et d’obtenir des informations originales sur des mécanismes régulateurs d’une grande importance
Retinoic Acid (RA) plays a critical role in many cellular processus through regulatory effects on cellular differentiation, proliferation and apoptosis. This proprety is at the basis of RA therapy in the treatment of several diseases and cancers such as Acute Promyelocytic Leukemia. Deciphering how RA controls the expression of specific subsets of genes is therefore a permanent challenge in oncology. The effects of RA are mediated in vivo by the retinoic acid receptor (RAR), which consistsof three subtypes. A new concept has recently emerged according to which phosphorylation of RARs by different kinases is a necessary step in the regulation of their function. In this context, the specific aim of this thesis was the elucidation of the molecular mechanisms of the regulation of RAR mediated by phosphorylation. In particular, we focused on two aspects, the effects of phosphorylation of the ligand binding domain (LBD) and the effects on the N-terminal domain (NTD). In the case of the LBD, phosphorylation enhanced binding to cyclin H, a component of the TFIIH transcription factor, while phosphorylation of the NTD decreased binding to vinexinB, a corepressor protein. We used molecular dynamics simulations to characterize the structural dynamics of these proteins in both phosphorylated and unphosphorylated states and to quantify theirinteractions. From this project, we were able to define the molecular basis of the communication between RA-induced phosphorylation cascades and regulatory mechanisms of high importance

Au niveau de la synapse, la liaison des neurotransmetteurs aux récepteurs membranaires induit l’ouverture de canaux ioniques. Le Récepteur de la Glycine (RGly) est un récepteur ionotrope impliqué dans des troubles neuronaux tels que l’addiction, la douleur chronique, ou l’hyperekplexie ; pour cette raison il est important de développer des nouveaux traitements ciblant ce récepteur. Nous avons utilisé des simulations de Dynamiques Moléculaire (DM) et d’électrophysiologie numérique afin d’évaluer la fonction des structures du RGly disponibles et montré qu’aucune d’entre elles ne satisfait les propriétés fonctionnelles de l’état ouvert. Grâce aux simulations de DM, nous avons caractérisé une nouvelle conformation du RGly, qui est compatible avec cet état. Nous avons souligné le rôle majeur des portails latéraux pour la perméation des ions. Nous avons proposé un protocole, nommé pharmacologie dépendante de l’état, pour identifier des molécules modulatrices de protéines allostériques
Signals within neurons are mostly transmitted through chemical synapses. Signal transduction arises from the binding of neurotransmitters to membrane receptors in order to open ion channels. The Glycine Receptor (GlyR) is an ionotropic receptor which is involved in several neurological disorders such as addiction, chronic pain, or hyperekplexia. Because of its implication in human diseases, it is interesting to design novel drugs targeting this receptor. We used Molecular Dynamics (MD) simulations and computational electrophysiology to probe the function of available GlyR structures. We showed that none of the experimental structures display the physiological behavior of the conductive state. Using MD simulations, we captured a novel conformation of the GlyR compatible with a conductive state and demonstrated the importance of lateral portals for ionic permeation. Lastly, we proposed an original protocol, named state-based pharmacology, to discover modulators of allosteric proteins

Die vorliegende Arbeit befasst sich mit dem Gebiet allosterischer Modulation des muscarinischen M2 Rezeptors. Allosterische Liganden beeinflussen das Bindungsverhalten eines orthosterischen Liganden (Agonisten oder Antagonisten) an die klassische Bindungsstelle des muscarinischen Rezeptors, indem sie seine Affinität entweder erhöhen(positive Kooperativität) oder erniedrigen (negative Kooperativität). Die allosterische Bindungsstelle befindet sich extrazellulär am Eingang der Rezeptor-Bindungstasche. Sie ist weniger konserviert als die orthosterische Bindungsdomäne, die tiefer im Rezeptorkanal zwischen den sieben transmembranalen Domänen lokalisiert ist. Demzufolge ist die Entwicklung subtyp-spezifischer allosterisch wirkenden Liganden leichter als subtypspezifischer Agonisten oder Antagonisten. Die Subtypselektivität kann darüber hinaus über unterschiedliche Kooperativitäten zwischen dem orthosterischen und allosterischen Liganden an verschiedenen muscarinischen Subtypen erreicht werden. Ein am M1-Rezeptor mit Acetylcholin positiv kooperativer allosterer Modulator, der sich an anderen muscarinischen Subtypen neutral kooperativ verhält, könnte z.B. für die Therapie von Morbus Alzheimer eingesetzt werden. Bisquartäre Ammoniumsalze des Strychnos-Alkaloids Caracurin-V gehören zu den potentesten allosterischen M2-Liganden. Die relative Stellung der aromatischen Indolringe und der Abstand zwischen den positiv geladenen Stickstoffatomen (ca. 10) in dem sehr starren Caracurin-V-Ringsystem definieren den Pharmakophor für potente allosterische Modulatoren. Caracurin-V-Salze sind strukturell sehr verwandt mit den starken Muskelrelaxantien Toxiferin-I und Alcuronium und besitzen vermutlich selbst neuromuskulär-blockierende Eigenschaften, was ihre Anwendung in der pharmakologischen Forschung einschränken würde. Reduktion des Caracurin-V-Ringsystems auf die wesentlichen Pharmakophorelemente könnte zu allosterisch wirksamen Verbindungen mit vernachlässigbarer muskelrelaxierender Wirkung führen. Ziel dieser Arbeit war die Synthese und pharmakologische Testung von Derivaten eines neuen, von Caracurin V abgeleiteten, heterocyclischen Ringsystems. Das neue gewünscht 6,7,14,15-Tetrahydro[1,5]diazocino[1,2-a:6,5-a]-diindole-Ringsystem(6) wurde in einer intermolekularen N-Alkylierung von zwei Molekülen Bromethylindol 5 aufgebaut. Die Ausgangsverbindung 5 konnte aus dem Indolylessigsäuremethylester 3 durch Reduktion der Estergruppe zum Alkohol und anschließende Substitution durch Brom dargestellt werden. Der bekannte Ester 3 wurde ausgehend von Tryptamin erhalten. Die dreistufige Synthese umfasste N-Dibenzylierung, Einführung der Malonestergruppe am C-2 von Indol und anschließende Demethoxycarbonylierung. Die Totalsynthese des neuen Pentacyclus ist im Schema 24 dargestellt. Die 3D-Struktur des neuen Ringgerüstes konnte mit Hilfe von NMR-Spektroskopie und semiempirischen Rechnungen (AM1) aufgeklärt werden. Verbindung 6 liegt in Lösung in einer verdrehten Wanne-Konformation mit unsymmetrisch angeordneten Seitenketten vor. Um den Einfluss der Seitenkettenlänge des neuen Ringsystems auf die allosterische Wirksamkeit zu untersuchen, war es geplannt, die Ethylamin-Gruppen durch Methylamin-Einheiten zu ersetzen. Der entsprechende Syntheseplan bestand darin, das unsubstituierte Ringsystem in einer doppelten Mannich-Reaktion zu aminomethylieren. Der Ausgangsstoff für die Dimerisierung, Bromethylindol 32, wurde aus Indol-2-carbonsäure hergestellt. Die Synthese umfasste folgende Reaktionsschritte: Reduktion der Carboxylgruppe und Benzoylierung des resultierenden Alkohols, nucleophile Substitution mit Kaliumcyanid, alkalische Hydrolyse des Cyanids zu Indolacetessigsäure, erneute Reduktion zum Alkohol und abschließende Substitution mit Brom. Da Dimerisierungsversuche von 32 nur zur Bildung des HBr-Eliminierungsproduktes 33 führten, wurde das entsprechende Tosylat als Ausgangsstoff eingesetzt. Überraschenderweise entstand nicht das erwartete Diazocinodiindol-Ringgerüst, sondern ausschließlich ein isomeres, noch nicht bekanntes 6,7,14,15-Tetrahydro-15aH-azocino[1,2-a:6,5-b]diindol-Ringsystem 35. Die Bildung des neuen unsymmetrischen Ringsystems ist auf den ambidenten Charakter des Indolylanions zurückzuführen, das entweder am Sticksoff oder an C3 alkyliert werden kann. Umsetzung von 35 nach Mannich lieferte das bisaminoalkylierte Produkt 37, neben einer kleinen Menge der monoalkylierten Verbindung 36. Die Totalsynthese des zweiten Ringsystems ist im Schema 25 dargestellt. Um potentere Verbindungen zu erhalten, wurden beide Endstufen 6 bzw. 37 mit Methyliodid zu 14 bzw. 38 quaternisiert. 37 wurde zusätzlich mit Allylgruppen zu 39 substituiert. Die pharmakologische Testung von 14, 37, und 38 erfolgte über Radioligandbindungsstudien an Membransuspensionen der Herzventrikel des Hausschweins. Der allostere Effekt der Testverbindungen wurde über die Hemmung der Dissoziation von [3H]-N-Methylscopolamin([3H]-NMS) von den damit gesättigten Rezeptoren gemessen. Die erhaltenen EC50,diss-Werte geben die Konzentration des allosteren Modulators an, bei der die [3H]-NMS-Dissoziation auf die Hälfte des Kontrollwertes reduziert ist. Sie sind ein Maß für die Affinität der Testsubstanzen zur allosterischen Bindungsstelle des M2 Rezeptors. Für die einzige Verbindung mit dem Diazocinodiindole-Ringsystem 14 wurde ein EC50,diss-Wert von 54 nM gemessen. Da 14 über vier Benzylsubstituenten verfügt, kann seine Bindungsaffinität am besten mit der von Dibenzylcaracurinium-Dibromid verglichen werden, die ganz ähnlich ist (69 nM). Aufgrund der Tatsache, dass die Verkleinerung des NSubstituenten am Caracurin-V-Gerüst zur erheblichen Steigerung der allosterischen Potenz führte, ist zu erwarten, dass der Austausch der voluminösen Benzylgruppen von 14 durch z.B. Methyl- oder Allylsubstituenten, eine deutliche Affinitätssteigerung bewirken würde. Damit scheint die allosterische Potenz des neuen Ringsystems mindestens genauso gut zu sein, wie die von Caracurin V. Die beiden Vertreter des Azocinodiindol-Ringsystems, 38 und 39, sind bereits mit den Gruppen substituiert, die die beste allosterische Potenz bei dem Caracurin-V-Ringsystem zeigten (Methyl- und Allyl). Ihre EC50,diss-Werte (35 nM für 38, 48 nM für 39) sprechen jedoch für eine ca. 4-fach schwächere Bindungsaffinität als die der entsprechenden Caracurine, was vermutlich auf einen anderen Abstand zwischen den quartären Stickstoffatomen und eine andere relative Stellung der Indolaromaten in den beiden Ringsystemen zurückzuführen ist. Anders als die entsprechenden Caracurin-V-Salze, sind 38 und 39 negativ kooperativ mit dem Antagonisten [3H]NMS. Zusammenfassend lässt sich feststellen, dass von den beiden neu synthetisierten heterocyclischen Ringsystemen das direkt von Caracurin V abgeleitete Tetrahydro- [1,5]diazocino[1,2-a:6,5-a]diindol eine bessere und vielversprechende Leitstruktur für die Entwicklung neuer potenter allosterischen Liganden des M2-Rezeptors darstellt. Weitere synthetische Arbeiten an dem Ringsystem wie z.B. Variation des Sticksstoffsubstituenten und der Seitenkettenlänge sollten zu einer Steigerung der Bindungsaffinität in den subnanomolaren Bereich führen. Darüber hinaus sind die Ergebnisse der pharmakologischen Testung an dem muskulären Typ des nicotinischen Acetylcholinrezeptors abzuwarten
The study deals with the area of the allosteric modulation of the muscarinic M2 receptors. The allosteric modulators have an influence on binding of orthosteric ligands (agonists and antagonists) to the classical orthosteric binding site of the muscarinic M2-receptors. The modulators are able to enhance (positive cooperativity) or decrease (negative cooperativity)the affinity of ligands to the orthosteric binding site. The allosteric binding site is located at the entrance of the receptor binding pocket. It is less conserved than the orthosteric binding site which is located in a narrow cavity created by the seven transmembrane domains. Consequently, development of subtype selective allosteric ligands is easier than subtypeselective muscarinic agonists or antagonists. Furthermore, subtype selectivity can be achieved by differently cooperative interactions between the allosteric and orthosteric ligand at different receptor subtypes. For example, the allosteric modulators that are positively cooperative with ACh at M1 receptors and neutrally cooperative at the other receptor subtypes could be beneficial for treatment of the Alzheimer’s disease. Bisquaternary analogues of the Strychnos alkaloid caracurine V are among the most potent allosteric modulators of muscarinic M2-receptors. The very rigid ring skeleton comprises the pharmacophoric elements of two positively charged nitrogens at an approximate distance of 10 surrounded by two aromatic ring systems in a distinct spatial arrangement. Owing to the close structural relationship of caracurine V salts to the strong muscle relaxants toxiferine and alcuronium, they are likely to exhibit neuromuscular blocking activity, which would limit their usefulness as research tools and make the therapeutical use impossible. Reduction of the caracurine V ring skeletons to structural features responsible for good allosteric potency could possibly lead to compounds with negligible neuromuscular blocking activity and very high affinity to the allosteric binding site at M2 receptor. Thus, the aim of this study was to synthesize and pharmacologically evaluate analogues of a novel heterocyclic ring system, which comprises the pharmacophoric elements mentioned previously. The key step of the synthesis of the desired 6,7,14,15-tetrahydro[1,5]diazocino[1,2-a:6,5-a]-diindole ring system (6) involved the intermolecular double N-alkylation of the bromoethylindole (5), which was prepared from the known indolyl methylacetate (3) by reduction of the ester group to alcohol and subsequent substitution by bromine. 3 could be prepared in three steps involving N,N-dibenzylation of tryptamine followed by introduction of the dimethyl malonate moiety at C-2 of indole ring and a subsequent demethoxycarbonylation. The total synthesis of 6,7,14,15-tetrahydro[1,5]diazocino[1,2-a:6,5-a]diindole ring system (6) is shown in Scheme 24. In order to examine the influence of the length of the side-chain on muscarinic activity,exchange of the ethylamine moieties of 14 by the methylamino groups was planned. This should be accomplished by dimerization of the unsubstituted 2-bromoethylindole (32), and subsequent Mannich aminomethylation of the resulting unsubstituted pentacyclic ring. The total synthesis of the 6,7,14,15-tetrahydro-15aH-azocino[1,2-a:6,5-b]diindole ring system(35) is shown in Scheme 25. 32 was prepared from indole-2-carboxylic acid in six steps involving reduction of the acid to the corresponding alcohol 26, benzoylation of 26 followed by nucleophilic substitution with KCN, hydrolysis of the cyanide 28 to indolyl acetic acid 29,reduction of 29 to the corresponding alcohol 30, and finally bromination of 30 to give the bromide 32. Since dimerization attempts of 32 provided only 2-vinylindole (33), the tosylate 34 was used as starting material for the intermolecular alkylation to give exclusively an isomeric pentacyclic ring system, 7,14,15-tetrahydro-15aH-azocino[1,2-a:6,5-b]diindole (35). The formation of the novel, asymmetric ring skeleton can be explained by the ambident nucleophilic character of the indolyl anion that can be alkylated either at nitrogen or at C-3 of indole ring. 35 was subjected to a Mannich reaction to give 2,13-dimethylaminoalkylated product 37 as well as small amounts of the 13-monosubstituted compound (36). The geometry of novel ring systems 6 was elucidated by means of NMR spectroscopy and semiempirical calculations. The diazocinodiindole ring skeleton of 6 exists in chloroform solution at room temperature in a twisted-boat conformation, as indicated by 600 MHz ROESY experiment, vicinal coupling constants within the eight-membered ring, and AM1 calculations. In order to obtain potent allosteric ligands, the new heterocycles 6 and 37 were quarternized with methyliodide to the corresponding ammonium salts 14 and 38, respectively. Additionally, the N,N -diallylsalts of 37 (compound 39) was prepared. The allosteric effect of 14, 38, and 39 on the dissociation of the orthosteric radioligand [3H]Nmethylscopolamine([3H]NMS) and their effects on [3H]NMS equilibrium binding were studied in homogenates of porcine heart ventricles. The concentration of an allosteric agent for a half-maximum effect on orthosteric ligand dissociation (EC50,diss) corresponds to a 50 % occupancy of the liganded receptors by the respective allosteric test compounds. Due to the presence of two benzyl groups on each nitrogen in the side chains of 14, its binding affinity can be best compared with that of N,N -dibenzylcaracurinium V dibromide (EC50,diss = 69 nM). Compound 14 exhibited the comparable affinity to N,N -dibenzylcaracurinium V dibromide with EC50,diss = 54 nM. This result suggested that replacement of the bulky benzyl groups of 14 by smaller substitutents will probably increase the allosteric potency, since dimethyl- and diallylcaracurinium salts showed a 5-fold increase of binding affinity relative to the dibenzyl analogue. Even though the new azocinodiindole ring system of 38 and 39, is not included in the caracurine V ring skeleton, it comprises the essentially pharmacophoric elements of allosteric potency. Due to the different spatial arrangements of the aromatic rings, as well as to different internitrogen distances in both ring systems, compound 38 and 39 exhibited 4-fold lower M2 binding affinity (EC50,diss = 35 and 48 nM, respectively) than the corresponding caracurine V analogues. This study deals with the synthesis of the first representative (Compound 6) of a novel pentacyclic ring system derived from caracurine V. The high allosteric potency of its dimethyl analogue reveals the [1,5]diazocino[1,2-a:6,5-a]-diindole ring system as a new promising lead structure for allosteric modulators of muscarinic M2 receptors. Future research will be focused on structural modifications of the new ring system in order to increase the affinity to the muscarinic receptors. Furthermore, the binding affinities of the new synthesized compounds to the muscle type of nicotinic ACh-receptor should reveal structural features responsible for the muscarinic/nicotinic selectivity

La prostaglandine E2 est une hormone lipidique produite abondamment dans le corps, incluant dans le rein où elle agit localement pour réguler les fonctions rénales. Un couplage à la protéine Gαs menant à une production d’AMPc a classiquement été attribué au récepteur EP4 de PGE2. La signalisation d’EP4 s’est cependant avérée plus complexe et implique aussi un couplage aux protéines sensibles à la PTX Gαi et des effets reliés aux β-arrestines. Il y a maintenant plusieurs exemples de l’activation sélective de voies de signalisation indépendantes par des ligands des récepteurs couplés aux protéines G (RCPG), et ce concept désigné sélectivité fonctionnelle pourrait être exploité dans le développement de nouveaux médicaments plus spécifiques et efficaces. Dans une première étude, la puissance et l’activité intrinsèque d’une série de ligands d’EP4 pour l’activation de Gαs, Gαi et de la ß-arrestine ont été systématiquement déterminées relativement au ligand endogène PGE2. Dans ce but, trois essais de transfert d’énergie de résonance de bioluminescence (BRET) ont été adaptés pour évaluer les différentes voies dans des cellules vivantes. Nos résultats montrent une sélectivité fonctionnelle importante parmi les agonistes évalués et ont une implication pour l’utilisation d’analogues de la PGE2 dans un contexte expérimental et possiblement clinique, puisque leur spectre d’activité diffère de l’agoniste naturel. La méthodologie basée sur le BRET utilisée lors de cette première évaluation systématique d’une série d’agonistes d’EP4 devrait être applicable à l’étude d’autres RCPG. Dans une deuxième étude, des peptides reproduisant des régions juxtamembranaires extracellulaires du récepteur EP4 ont été conçus selon le raisonnement que des peptides ciblant des régions éloignées du site de liaison du ligand naturel ont le potentiel de ne moduler qu’une partie des activités du récepteur. L’insuffisance rénale aiguë est une complication médicale grave caractérisée par un déclin brusque et soutenu de la fonction rénale et pour laquelle il n’y a pas de traitement efficace à l’heure actuelle. Nos résultats montrent que le peptidomimétique dérivé d’EP4 optimisé (THG213.29) améliore significativement les fonctions rénales et les changements histologiques dans une insuffisance rénale aiguë induite par cisplatine ou par occlusion des artères rénales dans des rats Sprague-Dawley. Le THG213.29 ne compétitionnait pas la liaison de la PGE2 à EP4, mais modulait la cinétique de dissociation de la PGE2, suggérant une liaison à un site allostérique d’EP4. Le THG213.29 démontrait une sélectivité fonctionnelle, puisqu’il inhibait partiellement la production d’AMPc induite par EP4 mais n’affectait pas l’activation de Gαi ou le recrutement de la ß-arrestine. Nos résultats indiquent que le THG213.29 représente une nouvelle classe d’agent diurétique possédant les propriétés d’un modulateur allostérique non-compétitif des fonctions du récepteur EP4 pour l’amélioration des fonctions rénales suite à une insuffisance rénale aiguë.
Prostaglandin E2 (PGE2) is a lipid hormone mediator widely produced in the body, including in the kidney where it acts locally to regulate renal function. Classically, the PGE2 receptor EP4 has been classified as coupling to the Gαs subunit, leading to intracellular cAMP increases. However EP4 signaling has been revealed to be more complex and also involves coupling to PTX-sensitive Gαi proteins and ß-arrestin mediated effects. There are now many examples of selective activation of independent pathways by G-protein coupled receptor (GPCR) ligands, a concept referred to as functional selectivity that could be exploited for the development of more specific and efficacious drugs. In a first study, the potencies and efficacies of a panel of EP4 ligands were systematically determined for the activation of Gαs, Gαi and ß-arrestin relative to the endogenous ligand PGE2. For this purpose, three bioluminescence resonance energy transfer (BRET) assays were adapted to evaluate the respective pathways in living cells. Our results suggest considerable functional selectivity among the tested, structurally related agonists and have implications for the use of PGE2 analogues in experimental and possibly clinical settings, as their activity spectra on EP4 differ from that of the native agonist. The BRET-based methodology used for this first systematic assessment of a set of EP4 agonists should be applicable for the study of other GPCRs. In a second study, peptides were derived from extracellular juxtamembranous regions of the EP4 receptor following the rationale that peptides that target regions of the receptor remote of the ligand-binding site might modulate a subset of the EP4-mediated activities. Acute renal failure is a serious medical complication characterized by an abrupt and sustained decline in renal function and for which there is currently no effective treatment. Our results show that the optimized EP4-derived peptidomimetic THG213.29 significantly improved renal functions and histological changes in acute renal failure induced by either cisplatin or renal artery occlusion in Sprague-Dawley rats. THG213.29 did not displace PGE2 binding to EP4, but modulated PGE2 binding dissociation kinetics, indicative of an allosteric binding mode. THG213.29 exhibited functional selectivity, as it partially inhibited EP4-mediated cAMP production but did not affect Gαi activation or ß-arrestin recruitment. Our results demonstrate that THG213.29 represents a novel class of diuretic agent with noncompetitive allosteric modulator effects on EP4 receptor function for improving renal function following acute renal failure.

碩士
國立中興大學
化學系所
106
In the first part of this thesis will describe the importance of sphingosine in different kinds of human diseases. Because of the requirement of sphingosine for biological research and the expensive cost of sphingosine, encouraged us to establish a concise method to synthesize sphingosine. The most important point is that we chose phytosphingosine, which is similar in structure to sphingosine as the starting material and it is cost-effective. We successfully developed two synthetic methods for sphingosine from phytosphingosine by using two different amine-protective pathways. In the second part of this thesis would describe the global prevalence and characteristics of coronaviruses. Thus we chose the important amino acid (W43) at the interface of the N-terminal domain of CoV N protein dimer which is highly conserved and it could be a potential drug binding position. We synthesized four kinds of ligands from commercially available 5-hydroxyindole. These ligands can bind with the interface of the dimer by the allosteric modulation effect. We found the ligand 34 could be deeper into the interface than the other ligands by subsequent experiments. Ligands 34 was also confirmed to have the oligomerization properties of MERS-CoV N protein. In the third part of this thesis would describe the toxicity of lipid A in human body. However, lipid A with a reduced number of acyl chains can serve as an inhibitor of immune activation and these inhibitors could prevent the harmful effect causing by bacterial infections in clinical trials. The point is that we use the same glucosamine salt 66 to get the disaccharide. Then we synthesize the derivative 61 of lipid A and it could provide a method of synthesizing the target lipid A 49 in the future.

The phosphatidylinositol-3-kinase α (PI3Kα) is a heterodimeric enzyme that is composed of a p85α regulatory subunit and a p110α catalytic subunit. PI3Kα plays a critical role in cell survival, growth and differentiation, and is the most frequently mutated pathway in human cancers. The PI3Kα pathway is also targeted by many viruses, such as the human immunodeficiency virus (HIV-1), the herpes simplex virus 1 (HSV-1) or the influenza A virus, to create favourable conditions for viral replication. The regulatory p85α stabilizes the catalytic p110α, but keeps it in an inhibited state. Various ligands can bind to p85α and allosterically activate p110α, but the mechanisms are still ill-defined. Intriguingly, p85α also binds to, and activates, the PTEN phosphatase, which is the antagonist of p110α. Previous studies indicated that only p85α monomers bind to the catalytic p110α subunit, whereas only p85α dimers bind to PTEN. These findings suggest that the balance of p85α monomers and dimers regulates the PI3Kα pathway, and that interrupting this equilibrium could lead to disease development. However, the molecular mechanism for p85α dimerization is controversial, and it is unknown why PTEN only binds to p85α dimers, whereas p110α only binds to p85α monomers. Here we set out to elucidate these questions, and to gain further understanding of how p85α ligands influence p85α dimerization and promote activation of p110α. We first established a comprehensive library of p85α fragments and protocols for their production and purification. By combining biophysical and structural methods such as small angle X-ray scattering, X-ray crystallography, nuclear magnetic resonance, microscale thermophoresis, and chemical crosslinking, we investigated the contributions of all p85α domains to dimerization and ligand binding. Contrarily to the prevailing thought in the field, we find that p85α dimerization and ligand recognition involves multiple domains, including those that directly bind to and inhibit p110α. This finding allows us to suggest a molecular mechanism that links p85α dimerization and allosteric p110α activation through ligands.

Selected nucleic acid binding species (aptamers) have been shown to undergo conformational changes in the presence of ligands, and have been adapted to function as biosensors. We were interested in whether the secondary structures of aptamers could be rationally engineered to undergo ligand dependent conformational changes. To this end, we used rational and computational design methods to generate a number of aptamer biosensors. First, we built upon previous work that showed that antisense oligonucleotides bearing reporter moieties could be used to denature aptamers. Upon addition of ligands, the conformational equilibrium is shifted towards release of the antisense oligonucleotide and a concomitant increase in fluorescence. We attempted to adapt this format to the potential detection of ricin, but were unsuccessful. In order to better evaluate rational designs, we attempted to use computational modeling methods. Again, aptamer biosensors have previously been engineered based on ligand-induced reorganization of secondary structure (as opposed to oligonucleotide displacement), a so-called 'slip-structure' model. We developed an algorithm to evaluate different lisp structures, predicted both aptamers and aptazymes that should have undergone ligand-dependent changes in conformation, and experimentally evaluated the computationally predicted sequences. A number of robust biosensors that could respond to the cytokine VegF and the small molecule flavin were discovered. The computational model was further adapted to an aptamer biosensor that underwent a larger conformational change upon ligand-binding, an antiswitch. In this model, binding of the ligand stabilizes one hairpin structure at the expense of a competing structure (as opposed to merely changing the register of the hairpin as in the previously described slip structure model). Again, we were able to computationally identify a number of antiswitches that upon synthesis were responsive to the ligand theophylline. Finally we again attempted to use rational design methods to optimize not just the degree of signal but also the kinetic performance of aptamer biosensors. To this end, we developed biosensors that signaled within seconds the presence of the coagulation protein thrombin.
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The glycine receptor (GlyR) is a ligand-gated ion channel member of the Cys-loop receptor superfamily, responsible for inhibitory neurotransmission in the brain and spinal cord. Zinc is a potent allosteric modulator of GlyR function, enhancing GlyR activity at low nM to 10[mu]M concentrations while inhibiting GlyR activity at higher concentrations. We investigated sources of contaminating zinc, identifying low nM levels of zinc in ultrapure H₂O, powdered reagents used in the preparation of common electrophysiological buffers, and in polystyrene pipets. These low levels of zinc were capable of enhancing GlyR function. These findings suggest that without checking for this effect using a zinc-chelator such as tricine, one cannot assume that responses elicited by glycine applied alone are not necessarily also partially due to some level of allosteric modulation by zinc. Taurine-activated GlyR may have a role in the rewarding effects of drugs of abuse. Zinc is found at GlyR-potentiating concentrations throughout the nervous system, so we examined the combinatorial effects of zinc with drugs of abuse on taurine-activated GlyR to mimic in vivo conditions. Whole cell recordings revealed that zinc potentiation of saturating taurine-generated currents decreased further potentiation by drugs of abuse, indicating no synergistic effects on efficacy when receptors are saturated with taurine as may be seen during synaptic events in vivo. Finally, we utilized phage display to identify novel peptide modulators of the GlyR. We tested 26 peptides against [alpha1beta] GlyRs, identifying peptides with various levels of activity on GlyR function. We demonstrated that these modulators were zinc-dependent, as their effects on GlyR activity were abolished in the presence of the zinc-chelating agent tricine. Together, these data indicate the importance of accounting for the effects of zinc when studying the function of the GlyR, as even low levels of zinc that can be found as contaminants in labware and buffers can affect GlyR function and responses to various allosteric modulators, including drugs of abuse.
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Allosteric regulation of proteins by reversible ligand binding is essential for regulation of fundamental biological processes. The mechanism by which a binding event alters the function of a distant site in a protein is only poorly understood. In this thesis, I use the Tetracycline Repressor (TetR) as a model system to study ligand induced allostery. The transcription of genes encoding the resistance to the antibiotic, tetracycline (Tc), is repressed by TetR, which is a homodimeric alpha-helical protein possessing a small N-terminal DNA binding domain (DNB domain) and a larger C-terminal tetracycline binding and dimerization domain (TBD domain). Based on previous structural and thermodynamic studies, the DNB domains are thought to exist in two stable, distinct conformations. One conformation is able to bind the Tc resistance operator sequence (tetO) with high affinity, while the other, which is induced by Tc binding, binds very weakly. While most previous studies on TetR have focused on the effects of Tc binding on the DNB domain conformation, here I have investigated the role of the DNB domain in modulating Tc binding. By introducing destabilizing mutations into the DNB domain I ascertained that the conformation and stability of the DNB domain plays an important role in determining Tc binding affinity. I also discovered that in the absence of ligand, the DNB domain exists in an unstable and flexible state with respect to the TBD domain. However, Tc binding to the TBD domain stabilizes the DNB domain, causing it to fold cooperatively with the TBD domain. I have discovered that the behavior of previously isolated non-inducible mutants is caused by the inability of Tc to stabilize the DNB domain in these mutants. Furthermore, reverse TetR mutants, which bind DNA better in the presence of Tc have an unfolded DNB domain that is only partially stabilized by Tc binding. My work suggests a new comprehensive, Tc induced stabilization and domain cooperativity model that can describe the mechanism of allostery in TetR and previously unexplainable mutants. A practical outcome of this research is the creation of a Tc induced folding switch that can be exploited to control the in vivo degradation of a protein of interest.

Antibiotic resistance is a worsening threat to human health. Increasing our understanding of the mechanisms causing this resistance will be of great benefit in designing methods to evade resistance and in developing new classes of antibiotics. In this thesis, I have used the TetR Family Transcriptional Regulators (TFRs), which constitute one of the largest antibiotic resistance regulator families, as a model system to study the structure, function and evolution of antibiotic resistance determinants. I performed a thorough examination of the variation and conservation seen in TFR sequences and structures using computational approaches. Through structure comparison, I have identified the most conserved features shared by the TFR family that are crucial for their stability and function. Based on my findings on conserved TFR structural features, a quantitative assay of binding affinity determination was developed. Through sequence comparison and a residue contact map method, I discovered the existence of a conserved residue network that correlates well with the known allostery pathway of TetR. This predicted allosteric communication network was experimentally tested in TtgR. I have also developed methods to identify TFR operator sequences through genomic comparisons and validated my prediction through experiments. In addition, I have developed an in vivo system that can be used to identify and characterize proteins that mediate resistance to almost any antibiotic. This system is simple, fast, and scalable for high-throughput applications, and could be used to discover a wide range of novel antibiotic resistance mechanisms. The principles that I applied to the TFR family could also be applied to other protein families.

The fidelity of biological processes and reactions, inspite of the widespread diversity, is programmed by highly specific physico-chemical principles. This underlines our basic understanding of different interesting phenomena of biological relevance, ranging from enzyme specificity to allosteric communication, from selection of fold to structural organization / states of oligomerization, from half-sites-reactivity to reshuffling of the conformational free energy landscape, encompassing the dogma of sequence-structure dynamics-function of macromolecules. The role of striking an optimal balance between rigidity and flexibility in macromolecular 3D structural organisation is yet another concept that needs attention from the functional perspective. Needless to say that the variety of protein structures and conformations naturally leads to the diversity of their function and consequently many other biological functions in general. Classical models of allostery like the ‘MWC model’ or the ‘KNF model’ and the more recently proposed ‘population shift model’ have advanced our understanding of the underlying principles of long range signal transfer in macromolecules. Extensive studies have also reported the importance of the fold selection and 3D structural organisation in the context of macromolecular function. Also ligand induced conformational changes in macromolecules, both subtle and drastic, forms the basis for controlling several biological processes in an ordered manner by re-organizing the free energy landscape. The above mentioned biological phenomena have been observed from several different biochemical and biophysical approaches. Although these processes may often seem independent of each other and are associated with regulation of specialized functions in macromolecules, it is worthwhile to investigate if they share any commonality or interdependence at the detailed atomic level of the 3D structural organisation. So the nagging question is, do these diverse biological processes have a unifying theme, when probed at a level that takes into account even subtle re-orchestrations of the interactions and energetics at the protein/nucleic acid side-chain level. This is a complex problem to address and here we have made attempts to examine this problem using computational tools. Two methods have been extensively applied: Molecular Dynamics (MD) simulations and network theory and related parameters. Network theory has been extensively used in the past in several studies, ranging from analysis of social networks to systems level networks in biology (e.g., metabolic networks) and have also found applications in the varied fields of physics, economics, cartography and psychology. More recently, this concept has been applied to study the intricate details of the structural organisation in proteins, providing a local view of molecular interactions from a global perspective. On the other hand, MD simulations capture the dynamics of interactions and the conformational space associated with a given state (e.g., different ligand-bound states) of the macromolecule. The unison of these two methods enables the detection and investigation of the energetic and geometric re-arrangements of the 3D structural organisation of macromolecule/macromolecular complexes from a dynamical or ensemble perspective and this has been one of the thrust areas of the current study. So we not only correlate structure and functions in terms of subtle changes in interactions but also bring in conformational dynamics into the picture by studying such changes along the MD ensemble. The focus was to identify the subtle rearrangements of interactions between non-covalently interacting partners in proteins and the interacting nucleic acids. We propose that these rearrangements in interactions between residues (amino acids in proteins, nucleic acids in RNA/DNA) form the common basis for different biological phenomena which regulates several apparently unrelated processes in biology. Broadly, the major goal of this work is to elucidate the physico-chemical principles underlying some of the important biological phenomena, such as allosteric communication, ligand induced modulation of rigidity/flexibility, half-sites-reactivity and so on, in molecular details. We have investigated several proteins, protein-RNA/DNA complexes to formulate general methodologies to address these questions from a molecular perspective. In the process we have also specifically illuminated upon the mechanistic aspects of the aminoacylation reaction by aminoacyl-tRNA synthetases like tryptophanyl and pyrrolysyl tRNA synthetase, structural details related to an enzyme catalyzed reaction that influences the process of quorum sensing in bacteria. Further, we have also examined the ‘dynamic allosterism’ that manipulates the activity of MutS, a prominent component of the DNA bp ‘mismatch repair’ machinery. Additionally, our protein structure network (PSN) based studies on a dataset of Rossmann fold containing proteins have provided insights into the structural signatures that drive the adoption of a fold from a repertoire of diverse sequences. Ligand induced percolations distant from the active sites, which may be of functional relevance have also been probed, in the context of the S1A family of serine proteases. In the course of our investigation, we have borrowed several concepts of network parameters from social network analysis and have developed new concepts. The Introduction (Chapter-1) summarizes the relevant literature and lays down a suitable background for the subsequent chapters in the thesis. The major questions addressed and the main goal of this thesis are described to set an appropriate stage for the detailed discussions. The methodologies involved are discussed in Chapter-2. Chapter-3 deals with a protein, LuxS that is involved in the bacterial quorum sensing; the first part of the chapter describes the application of network analysis on the static structures of several LuxS proteins from different organisms and the second part of this chapter describes the application of a dynamic network approach to analyze the MD trajectories of H.pylori LuxS. Chapter-4 focuses on the investigation of human tryptophanyl-tRNA synthetase (hTrpRS), with an emphasis to identify ligand induced subtle conformational changes in terms of the alternation of rigidity/flexibility at different sites and the re-organisation of the free energy landscape. Chapter-5 presents a novel application of a quantum clustering (QC) technique, popular in the fields of pattern recognition, to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. The protein structure network (PSN) in the earlier studies were constituted on the basis of geometric interactions. In Chapters 6 and 7, we describe the networks (proteins+nucleic acids) using interaction energy as edges, thus incorporating the detailed chemistry in terms of an energy-weighted complex network. Chapter-6 describes an application of the energy weighted network formalism to probe allosteric communication in D.hafniense pyrrolysyl-tRNA synthetase. The methodology developed for in-depth study of ligand induced changes in DhPylRS has been adopted to the protein MutS, the first ‘check-point protein’ for DNA base pair (bp) mismatch repair. In Chapter-7, we describe the network analysis and the biological insights derived from this study (the work is done in collaboration with Prof. David Beveridge and Dr. Susan Pieniazek). Chapter-8 describes the application of a network approach to capture the ligand-induced subtle global changes in protein structures, using a dataset of high resolution structures from the S1A family of serine proteases. Chapter-9 deals with probing the structural rationale behind diverse sequences adopting the same fold with the NAD(P)-binding Rossmann fold as a case study. Future directions are discussed in the final chapter of the thesis (Chapter-10).

The dissertation is focused on the role of chemotaxis receptor played in the transmembrane signaling. The first project accomplished was to study the interaction between serine receptor and methyltransferase. As an effort to probe the regulation mechanism of methyltransferase CheR, Isothermal Titration Calorimetry (ITC) was applied to characterize any possible regulation associated allosteric effect between methyltransferase CheR's multiple interactions. It was found that methyltransferase CheR binds to its receptor docking site and substrate SAH independently, further experiments are proposed to explore the interaction between the receptor methylation region and methyltransferase, CheR. It is speculated that conformational change in the receptor upon ligand binding controls the accessibility of the receptor methylation region to methyltransferase. The second project was carried out as a continued effort to determine the receptor ligand binding activity in the ternary complex with the adaptor protein CheW and the histidine kinase CheA, and it was expected that some cooperativity between receptor dimers would be observed. Surprisingly, in the absence of the cytoplasmic signaling proteins, CheW and CheA, serine receptors exhibited negative cooperativity in ligand binding between dimers, and the negative cooperavtivity disappeared in detergent solution. For the first time, direct evidence was found as a strong support the transmembrane signaling mechanism that involves receptor clusters. Chemoreceptors form patches at the poles of bacteria in the presence and absence of signaling proteins, and the active interaction between receptor dimers could play a significant role in information integration when passing through the bacterial membrane. Experiments are also designed for further clarify the function of receptor cluster in the future.

Zahlreiche experimentelle Befunde lassen vermuten, dass G-Protein gekoppelte Rezeptoren (GPCR) nach ihrer Aktivierung einer ligandenselektiven Änderung der Rezeptorkonformation unterliegen. Ziel der vorliegenden Arbeit war es dieses Phänomen am Subtyp 2 der muskarinischen Acetylcholinrezeptoren (M2 AChR) zu untersuchen. Muskarinische Acetylcholinrezeptoren (mAChR) können in fünf Subtypen (M1-M5) unterschieden werden. Durch die Beteiligung der mAChR an zahlreichen physiologischen Prozessen stellen sie wichtige Zielstrukturen pharmakologischer Therapien dar. Da die orthosterische Ligandenbindestelle (= Bindestelle des endogenen Liganden) in allen fünf Subtypen hoch konserviert ist, wird ihr pharmakologischer Nutzen derzeit allerdings durch die unselektive Rezeptormodulation und dem damit verbundenen Auftreten unerwünschter Arzneimittelwirkungen stark limitiert. Ein Ansatz zur Erzielung subtypselektiver Effekte besteht in der Verwendung allosterischer Modulatoren. Da die allosterische Bindestelle der mAChR eine geringere Sequenzhomologie aufweist, können so gezielt einzelne Subtypen der mAChR reguliert werden. Der M2 AChR stellt hinsichtlich allosterischer Modulation ein gut charakterisiertes Modellsystem dar. Für ihn wurde bereits eine Vielzahl allosterischer Liganden entwickelt. Auch bitopische Liganden, die sowohl einen allosterischen als auch einen orthosterischen Anteil enthalten, wurden für den M2 AChR bereits beschrieben. Im ersten Teil der vorliegenden Arbeit wurden verschiedene FRET-Sensoren des M2 AChR generiert und charakterisiert. Als FRET-Paar wurden das cyan fluoreszierende Protein (CFP) und der niedermolekulare fluorescein-basierte Fluorophor FlAsH (fluorescein arsenical hairpin binder) gewählt. CFP wurde in den Sensoren am Ende des C-Terminus angefügt. Die zur Markierung mit FlAsH nötige Tetracysteinsequenz wurde in verschiedenen Bereichen der dritten intrazellulären Rezeptorschleife (IL) eingebracht. Die auf diese Weise erstellten Re-zeptorsensoren trugen das Tetracysteinmotiv in der N terminalen (M2i3-N) bzw. in der C terminalen Region (M2i3-C) von IL 3. Die Charakterisierung der Rezeptorsensoren bezüglich Ligandenbindung, Gi-Protein Aktivierung und β-Arrestin2 Translokation ergab keine signifikanten Unterschiede zwischen M2i3-N, M2i3 C und M2CFP oder Wildtyp M2 AChR. Zunächst wurden sowohl unterschiedliche orthosterische, als auch allosterische Liganden hinsichtlich ihrer mittleren effektiven Konzentration und ihrer maximalen Wirkstärke an den Rezeptorsensoren untersucht. Mit Hilfe von FRET-Messungen konnte ein superago-nistisches Verhalten des orthosterischen Testliganden Iperoxo gezeigt werden. Die Eigenschaften der allosterischen Substanzen wurden durch Messung der Rezeptordeakti-vierungskinetik und des maximalen Hemmeffekts auf einen vorstimulierten Rezeptor charakterisiert. Alle allosterischen Liganden deaktivierten den vorstimulierten M2 AChR mit einer schnelleren Kinetik als Atropin. Die EC50-Werte der unterschiedlichen Substanzen waren unabhängig von der Markierungsposition im verwendeten Rezeptorsensor vergleich-bar. Ausnahmen bildeten die allosterischen Liganden JK 289, JK 338, ½ W84 und EHW 477, die liganden- und sensorabhängig unterschiedliche mittlere effektive Konzentrationen aufwie-sen. Bei der Untersuchung der Konformationsänderung des M2 AChR konnte kein liganden-selektiver Unterschied zwischen den FRET-Signalen für 19 getestete orthosterische Liganden beobachtet werden. Dies deutet darauf hin, dass alle orthosterischen Testliganden eine dem Acetylcholin (ACh) vergleichbare Änderung der M2 AChR Konformation induzier-ten. Um zu untersuchen, ob für die orthosterischen Testliganden eine Korrelation zwischen ihrer maximalen Wirkstärke hinsichtlich Rezeptoraktivierung in FRET-Experimenten und der Aktivierung nachgeschalteter Signalwege besteht, wurde die orthosterisch-vermittelte Translokation von β-Arrestin2 mit Hilfe der Konfokalmikroskopie bestimmt. Bis auf 5-Methyl-furmethiodid translozierten alle orthosterischen Liganden β-Arrestin2 in einem Ausmaß, das mit der maximalen Rezeptoraktivierung vergleichbar war. Dagegen rief 5 Methylfurmethiodid verglichen mit dem endogenen Liganden ACh zwar eine ca. halbmaximale Rezeptorakti-vierung, aber nur eine äußerst geringe β-Arrestin2 Translokation hervor. Im zweiten Teil der Arbeit wurde der Einfluss verschiedener Allostere auf eine ligandenselektive Konformationsänderung des M2 AChR untersucht. Die allosterischen Liganden JK 337 und Seminaph beeinflussten den M2i3-C Sensor signifikant stärker, als das M2i3-N Konstrukt. Dagegen zeigte EHW 477 eine stärkere Beeinflussung der Rezeptorkon-formation des M2i3-N-, als des M2i3-C Sensors. Dies erlaubt die Vermutung, dass JK 337 und Seminaph eine stärkere Bewegung unterhalb von Transmembrandomäne (TM) 6, als unterhalb von TM 5 hervorriefen. Die Ergebnisse für EHW 477 legen nahe, dass TM 5 eine größere Bewegung eingeht, als TM 6. FRET-basierte Untersuchungen der Einflüsse der allosterischen Testliganden auf nachgeschaltete Signalwege ergaben, dass sowohl die Akti-vierung des Gi Proteins, als auch die β-Arrestin2 Translokation selektiv durch einzelne allosterische Liganden beeinflusst werden. Auch ein Zusammenhang zwischen Rezeptor-aktivierung und der Regulation nachgeschalteter Signalwege war erkennbar. Allerdings waren auf Grund der Versuchsbedingungen keine quantitativen Aussagen möglich. Im Folgenden wurden die bitopischen Liganden Hybrid 1 und 2 (H 1, H 2) hinsichtlich ihres Effekts auf die Konformationsänderung des M2 AChR untersucht. Während eine Stimulation mit H 1 vergleichbare FRET-Signale an beiden Sensoren ergab, konnte mit H 2 weder am M2i3-N-, noch an M2i3-C Sensor eine FRET-Änderung detektiert werden. Um den mangeln-den Effekt der Hybridsubstanzen in FRET-mikroskopischen Untersuchungen aufzuklären, wurden verschiedene Ansätze gewählt: Mit kettenverlängerten Derivaten der Hybridsubstanzen konnte in FRET-Messungen eine Änderung des FRET-Signals detektiert werden. Die Entfernung des allosterischen Bausteins führte in FRET-Experimenten zu einer verglichen mit dem endogenen Liganden ACh etwa halbmaximalen Aktivierung beider Sensoren. Dagegen resultierte die Mutation der alloste-rischen Bindestelle in nachfolgenden FRET-Untersuchungen mit H 1 und H 2 in keiner Signaländerung des FRET-Ratio. Diese Beobachtungen führten zu der Annahme, dass die Linkerkette, die orthosterischen und allosterischen Baustein der Hybride miteinander verbindet, zu kurz war um eine gleichzeitige Bindung an die allosterische und orthosterische Bindestelle zu ermöglichen. Ein anderer Erklärungsansatz besteht darin, dass nach Bindung des Orthosters der Kanal zwischen orthosterischer und allosterischer Bindestelle durch die Konformationsänderung des Rezeptors verschlossen wird, weshalb keine dauerhafte, dualsterische Bindung der Hybridsubstanzen an den M2 AChR möglich ist. Im Rahmen der vorliegenden Arbeit ist es gelungen mittels FRET-Experimenten die Existenz einer ligandenselektiven Rezeptorkonformation des M2 AChR mit allosterischen Liganden nachzuweisen. Darüber hinaus konnte auch ein Bezug zum Auftreten einer funktionellen Selektivität mit allosterischen Liganden hergestellt werden. Die Untersuchung von 19 orthosterischen Liganden hinsichtlich ihres Einflusses auf die Rezeptorkonformation des M2 AChR ergab keinen Hinweis auf eine ligandenselektive Konformationsänderung. Die Betrachtung der orthosterisch-vermittelten Translokation von β-Arrestin2 zeigte, dass zwischen der Effizienz der orthosterischen Testliganden, den M2 AChR zu aktivieren und dem Ausmaß, in dem sie eine β Arrestin2 Translokation induzierten eine direkte Korrelation besteht. Lediglich 5-Methylfurmethiodid rief eine ungleich geringere β-Arrestin2 Translokation hervor, verglichen mit dem Ausmaß an Rezeptoraktivierung. Diese Beobachtung deutet auf die Existenz eines signaling-bias für diesen Liganden hin. Die Untersuchung der dualsterischen Liganden H 1 und 2 bezüglich ihrer Fähigkeit zur Rezeptoraktivierung ergab, dass erst durch eine Verlängerung der Linkerkette, durch die orthosterischer und alloste-rischer Baustein miteinander verbunden sind eine Konformationsänderung des M2 AChR hin zu einer aktiven Konformation erreicht werden kann. Es kann somit angenommen werden, dass in den ursprünglichen Hybridsubstanzen H 1 und H 2 eine zu kurze Linkerkette, durch die keine dualsterische Bindung der Hybride an die allosterische und orthosterische Bindestelle möglich ist, ursächlich für die mangelnde Rezeptoraktivierung des M2 AChR war
A large body of experimental evidence suggests that upon receptor activation G-protein coupled receptors are subject to ligandspecific changes of receptor conformation. The aim of this study was to investigate this phenomenon using the muscarinic M2 acetylcholine receptor (M2 AChR). Muscarinic acetylcholine receptors (mAChR) can be subdivided into five different subtypes (M1-M5). Their involvement in various physiological processes makes them an important target of pharma-cological therapies. With the orthosteric binding site (= binding site of the endogenous ligand) being highly conserved across all five mAChR subtypes, the unselective receptor modulation can lead to severe side effects. Thus the clinical use of drugs modulating muscarinic receptors is currently limited. Allosteric modulation is one attempt to achieve subtype-selective receptor regulation. Since the allosteric binding site of mAChR is less well conserved, it is possible to selectively target one mAChR subtype. As far as allosteric modulation is concerned, the M2 AChR represents a well characterized model with a large number of allosteric modulators being available. For the M2 AChR bitopic ligands which contain an allosteric as well as an orthosteric binding block have been developed as well. In the first part of this study several FRET-sensors of the M2 AChR were designed and characterized. The cyan fluorescent protein (CFP) was fused to the C-terminus of both sensors while the FlAsH (fluorescein arsenical hairpin binder) binding site was inserted into the N-terminal (M2i3-N) or the C terminal (M2i3-C) region of the third interacellular loop (IL). The receptor sensors were characterized concerning ligand affinity, activation of the Gi protein and -arrestin2 translocation and did not display any significant differences compared to the wildtype M2 or the M2 CFP receptor. Various orthosteric as well as allosteric ligands were investigated regarding their affinity and efficacy at both sensors. Using FRET-measurements iperoxo was proven to behave as a superagonist. The characteristics of the allosteric ligands were investigated by measuring the receptor deactivation kinetics and their maximum inhibitory effect on a pre-stimulated receptor. All allosteric test substances displayed faster deactivation kinetics compared to the antagonist atropine and similar EC50 values at both receptor sensors. When investigating the change of receptor conformation of the M2 AChR upon ligand binding there were no ligand selective differences in the FRET-signal detected for either of the 19 orthosteric ligands at both M2 sensors. This data suggest that all orthosteric ligands induced a change in receptor conformation comparable to acetylcholine (ACh). In order to correlate the efficacy of various orthosteric ligands to activate the M2 AChR in FRET-experiments with their effect on downstream signaling pathways, the translocation of  arrestin2 upon receptor activation with orthosteric ligands was investigated using confocal microscopy. Except for 5 methylfurmethiodide all orthosteric ligands induced -arrestin2 translocation to an extent which was comparable to the maximal receptor activation observed with each other ligand, respectively. In contrast 5-methylfurmethiodide evoked a half maximal receptor activation compared to the endogenous ligand ACh while only a minimal translocation of -arrestin2 was observed. The second aim of this study was to investigate the effects of allosteric ligands on the change of receptor conformation of the M2 AChR. The allosteric ligands JK 337 and seminaph more strongly influenced the M2i3-C than the M2i3-N, whilst EHW 477 behaved just the opposite way. This data suggest that the orthosteric ligands induce a conformation of the M2 AChR comparable to ACh. JK 337 and seminaph seem to evoke a greater movement underneath TM 6 compared to TM 5 whereas EHW 477 probably induces a larger movement beneath TM 5. The allosteric ligands were tested via FRET-measurements concerning their ability to activate the Gi protein and to translocate  arrestin2. The activation of the Gi protein as well as the -arrestin2 translocation were selectively influenced by all allosteric ligands. However, due to the experimental setup, a quantification of the effects was not possible. Furthermore the bitopic ligands hybrid 1 and 2 (H 1, H 2) were tested regarding their effect on the receptor conformation of the M2 AChR. While stimulation with H 1 induced FRET signals that were comparable for both receptor sensors, it wasn’t possible to detect any change in the FRET ratio neither of the M2i3-N nor of the M2i3-C with H 2. The lack of effect of H 1 and H 2 in the FRET-experiments was explored using two different approaches: Derivatives of H 1 and H 2, in which the carbon linker between the allosteric and the orthosteric building block had been elongated, were able to induce changes in the FRET ratio. Upon the removal of the allosteric building block a half-maximal activation of both receptor sensors could be detected. However, the mutation of the allosteric binding site did not result in any change of the FRET-signals upon stimulation of the receptor mutants with H 1 or H 2. These data suggest that the carbon linker, which connects the allosteric and the orthosteric building block, is not long enough to enable a simultaneous binding to the allosteric and the orthosteric binding site. Another explanation would be that upon binding of an orthoster the channel between the orthosteric and the allosteric binding site of the M2 AChR is closed because of the change in receptor conformation, hence a stable, dual-steric binding of the hybrid substances to the M2 AChR would not be possible. In the course of this study it was possible to prove the existence of a ligand selective receptor conformation of the M2 AChR with allosteric ligands using FRET-experiments. In addition a connection was found to the occurrence of a functional selctivity with allosteric ligands. The investigation of 19 orthosteric ligands regarding their influence on the receptor conformation of the M2 AChR did not reveal any evidence of the existence of a ligand selective change of the receptor conformation. Regarding the translocation of β arrestin2 induced by orthosteric ligands there was a direct correlation between the efficency of the orthosteric ligands to activate the receptor and the extend of β-arrestin2 translocation observed. With the only exception being 5-methylfurmethiodide which induced far less β arrestin2 translocation compared to the magnitude of the conformational change of the receptor. This data suggest the existence of a signaling bias for this ligand. The analysis of the dualsteric ligands H 1 and H 2 concerning their ability to activate the M2 AChR revealed that an activation of the M2 AChR could just be observed upon elongation of the linker which connects the orthosteric with the allosteric building block. This suggests that the short linker chain of the original hybrid substances inhibited a dualsteric binding to the orthosteric and the allosteric binding site and thus caused the difficency of H 1 and H 2 to activate the M2 AChR

Title: Computer modeling of ion protein interactions: Allosteric effects of phenolic ligands and ions on insulin hexamer structure Author: Vladimír Palivec Department: Department of Physical and Macromolecular Chemistry Faculty of Science UK Advisor: prof. RNDr. Pavel Jungwirth, DSc., IOCB AS CR, v.v.i. Advisor's email address: pavel.jungwirth@uochb.cas.cz Abstract: Insulin hexamer is an allosteric protein capable of undergoing conformational changes between three states: T6, T3R3, and R6. Transitions between them, as well as the formation of insulin hexamers, are mediated through binding of phenolic ligands or ions. This thesis presents a molecular dynamics study of allosteric behavior of insulin using empirical force fields. Two effects are closely inspected - cation (Zn2+ , Ca2+ , K+ , and Na+ ) binding to the insulin hexamers and a possible binding of two neurotransmitters - dopamine and serotonin to the phenolic pocket. The results show that high charge density cations (Zn2+ and Ca2+ ) are mostly localized in the B13 glutamate cavity, slow- down diffusion, while preventing other cations from entering. In contrast, low charge density cations (Na+ and K+ ) do not have this effect. Concerning neurotransmitters, dopamine does not bind to the phenolic pocket whereas serotonin binds in a similar way like...