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京都大学 / 新制・課程博士 / 博士(薬科学) / 甲第24558号 / 薬科博第175号 / 新制||薬科||19(附属図書館) / 京都大学大学院薬学研究科医薬創成情報科学専攻 / (主査)教授 土居 雅夫, 教授 竹島 浩, 教授 中山 和久 / 学位規則第4条第1項該当 / Doctor of Pharmaceutical Sciences / Kyoto University / DFAM

When applied to drug discovery, modern computational systems can provide insight into the highly complex systems underlying drug activity and predict compounds or targets of interest. Many tools have been developed for computer aided drug discovery (CADD), focusing on small molecule ligands, protein targets, or both. The aim of this thesis is the improvement of CADD tools for describing small molecule properties and application of CADD to several stages of drug discovery regarding two targets for the treatment of obesity and related diseases: the neuropeptide Y4 receptor (Y4R) and the melanocortin-4 receptor (MC4R). In the first chapter, the major categories of CADD are outlined, including descriptions for many of the popular tools and examples where these tools have directly contributed to the discovery of new drugs. Following the introduction, several improvements for encoding stereochemistry and signed property distribution are introduced and tested in scenarios meant to simulate applications in virtual high-throughput screening. Y4R and MC4R are both class A G-protein coupled receptors (GPCRs) with endogenous peptide ligands that play critical roles in the signaling of satiety and energy metabolism. So far, no structures from either receptor family have been experimentally elucidated. CADD was combined with high-throughput screening (HTS) to discover the first small molecule positive allosteric modulators (PAMs) of Y4R. Secondly, CADD techniques were used to model the interaction of Y4R and pancreatic polypeptide based on experimental results that elucidate specific binding contacts. Similar SB-CADD approaches were used to model the interaction of MC4R with its high affinity peptide agonist α-MSH. Due to its role in monogenic forms of obesity, these models were used to predict which residues directly participate in binding and correlate mutated residues with their potential role in the binding site.

Foram examinadas as propriedades conformacionais de um peptídeo (YRWPFGNHL-NH2) presente na primeira alça extra-celular do receptor AT1 do hormônio angiotensina II. Espectros de dicroísmo circular (CD) e fluorescência foram obtidos em solução aquosa (em função do pH e da temperatura), na presença de um solvente indutor de estrutura secundária (trifluoroetanol, TFE), e na presença de micelas carregadas negativamente (dodecil sulfato de sódio, SDS) ou zwitteriônicas (N-hexadecil-N,N-dimetil-3-amônio-1-propano sulfonato, HPS e lisofosfatidilcolina, liso-PC), e de bicamadas contendo um fosfolipídio zwitteriônico (1-palmitoil-2-oleoil fosfatidilcolina, POPC) ou uma mistura de POPC e um fosfolipídio carregado negativamente (ácido l-palmitoil-2-oleoil fosfatídico, POPA). O estudo por calorimetria de titulação permitiu analisar a termodinâmica da ligação. Espectros de CD indicaram uma estrutura flexível em solução aquosa, modulada pelo pH e pela temperatura. Na presença de TFE, de micelas, e de vesículas de POPC:POPA o peptídeo adquire estrutura secundária, sugerindo a presença de uma dobra beta. Espectros de fluorescência intrínseca (W3) mostraram um deslocamento do comprimento de onda máximo de emissão (λmax) para o azul na presença de micelas e de vesículas de POPC:POPA. Observou-se também um aumento da intensidade de fluorescência, exceto no caso de SDS. Esses resultados indicaram que o peptídeo interagiu com os agregados. Não se observou alteração da fluorescência na presença de POPC. Medidas de anisotropia de fluorescência mostraram que, quando ligado, o peptídeo toma-se mais imobilizado. Estudos de supressão de fluorescência empregando agentes supressores aquossolúveis e de membrana sugeriram que o W3 localiza-se próximo à interface bicamada-água. Os resultados mostraram que o peptídeo se liga a micelas zwitteriônicas e negativas, enquanto que, no caso de bicamadas (mais empacotadas), a ligação depende da presença de cargas negativas. Experimentos de calorimetria mostraram que o ΔH de ligação do peptídeo a vesículas é negativo, compatível com a ocorrência de interações eletrostáticas. Foram observadas diferenças qualitativas e quantitativas na ligação do peptídeo às micelas de HPS e liso-PC. A fim de examinar se essas diferenças eram devidas ao empacotamento molecular, foram obtidos espectros de ressonância paramagnética eletrônica de marcadores de spin intercalados nos dois sistemas. Diferenças foram observadas principalmente na região da cabeça polar, as quais poderiam ser responsáveis pela diferença de comportamento do peptídeo em ambos os agregados. Os resultados obtidos para a primeira alça extra-celular do receptor AT1 indicam que a sua conformação pode ser modulada pelo pH e pela polaridade do ambiente, que ela pode interagir com a membrana através de interações hidrofóbicas e eletrostáticas, e ainda que essa interação depende do grau de empacotamento da fase lipídica. Esses resultados estão de acordo com a visão de que domínios extra-membranares de GPCRs situam-se na interface membrana-água. As alterações conformacionais induzidas pelo meio, bem como pela interação entre domínios extra-membranares de GPCRs e a fase lipídica ou pela ligação do agonista, poderiam ter um papel no mecanismo molecular de transdução de sinal. / In this work the conformational properties of a peptide (YRWPFGNHL-NH2) whose sequence is present in the first extra-cellular loop of the angiotensin II AT1 receptor were examined. Circular dichroism (CD) and fluorescence spectra were obtained in aqueous solution (as a function of pH and temperature), in the presence of a secondary structure inducing solvent (trifluoroethanol, TFE), and in the presence of negatively charged (sodium dodecyl sulfate, SDS) or zwitterionic (N-hexadecyl-N,N-dimethyl-3-ammonio-1-propane sulfonate, HPS and lysophosphatidylcholine, liso-PC) micelles, and of bilayers containing a zwitterionic phospholipid (l-palmitoyl-2-oleoyl phosphatidylcholine, POPC) or a mixture of POPC and a negatively charged phospholipid (l-palmitoyl-2-oleoyl phosphatidic acid, POPA). Studies of titration calorimetry allowed the analysis of the binding thermodynamics. CD spectra indicated a flexible structure in aqueous solution, which was modulated by pH and temperature. In the presence of TFE, micelles and of POPC:POPA vesicles, the peptide acquired secondary structure, which is suggestive of a β turn. The intrinsic fluorescence spectra (W3) showed a blue-shift of the maximum emission wavelenght (λmax) in the presence of micelles and of POPC:POPA vesicles. An increase in fluorescence intensity was also observed, except in the case of SDS. These results indicated that the peptide interacted with the aggregates. No fluorescence changes were observed in the presence of POPC. Fluorescence anisotropy measurements showed that, when bound to the aggregates, the peptide becomes more immobilized. Fluorescence quenching studies using water soluble and membrane-bound quenchers suggested that W3 is located close to the water-bilayer interface. The results showed that the peptide binds to negativelly charged and zwitterionic micelles, while in the case of bilayers (which are more tightly packed) the binding depends on the presence of negative charges. Titration calorimetry showed that ΔH of peptide binding to the vesicles is negative, which is compatible with the ocurrence of eletrostatic interactions. Qualitative and quantitative differences in binding of the peptide to HPS and liso-PC micelles were observed. In order to examine whether these differences were due to molecular packing, electron paramagnetic resonance spectra of spin labels intercalated in both systems were obtained. Differences were observed, mainly in the polar head group region, that could be responsible for the different behaviour displayed by the peptide in both aggregates. The results obtained for the first extra-cellular loop of the AT1 receptor indicated that its conformation can be modulated by pH and by the polarity of the medium, and that it can interact with the membrane through hydrophobic and electrostatic interactions, and also that this interaction depends on the molecular packing of the lipid phase. These results are in aggrement with the idea that the GPCRs extra-membrane domains are located at the water-membrane interface. Conformational changes induced by the medium, as well as by the interaction between extra-cellular segments and the membrane or by ligand binding, could play a role in the molecular mechanism of signal transduction.

Les récepteurs couplés aux protéines G (RCPG) constituent l'une des plus grandes familles de gènes du génome des mammifères. Ils sont impliqués dans la plupart des processus physiologiques et physiopathologiques ce qui en a fait des cibles thérapeutiques de choix. GPR158 est un récepteur orphelin, dont on ne connaît pas de ligand, de la classe C des RCPG. Il partage 20% d'identité de séquence entre son domaine transmembranaire (TM) et celui du récepteur GABAB mais son domaine N-terminal est dépourvu du domaine Venus Flytrap (VFT), le domaine de liaison du ligand caractéristique des RCPG de la classe C, ce qui suggère que cette protéine a développé un autre mode de liaison de son ligand endogène (s'il existe). GPR158 est exprimé majoritairement au niveau du cerveau. De manière intéressante, son expression a été aussi décrite, dans des cribles à plus ou moins grande échelle, comme étant associée ou modifiée dans différentes conditions pathologiques dont 50% sont des maladies cancéreuses.À ce jour, on ne connait ni la fonction physiologique, ni les voies de signalisation de GPR158. Dans un premier temps, notre objectif était de comprendre la fonctionnalité de GPR158 en cherchant une activité constitutive de ce récepteur ou en essayant de générer des mutants, des récepteurs tronqués ou des récepteurs chimériques constitutivement actifs. Jusqu'à présent, nous n'avons pas réussi à avoir un récepteur actif, malgré les résidus des boucles intracellulaires et des domaines TM importants pour le couplage aux protéines G et pour l'activation des autres RCPG, qui sont conservés dans GPR158. Ce qui suggère que ce récepteur pourrait ne pas avoir une signalisation en lui même, et il régulerait ainsi l'activité d'autres RCPG. Dans le cas inverse, GPR158 aurait un mode de signalisation très original qui reste à découvrir. Puis nous avons cherché à comprendre le rôle physiologique lié aux trois motifs VCPWE, que nous avons identifiés au niveau du domaine C-terminal (C-ter), très long, de ce récepteur. Ces motifs sont bien conservés chez les différentes espèces et joueraient ainsi des rôles fonctionnels importants. À ce sujet, nous avons montré que le troisième motif s'associe spécifiquement avec la sous-unité Gαo, probablement activée, des protéines G. Et nous avons également identifié, un site d'interaction d'un régulateur de l'activité des protéines G, RGS7, au niveau du domaine C-ter de GPR158, en amont des motifs. Vu que Gαo est le substrat de RGS7, nous suggérons que Gαo lierait en même temps le domaine RGS de la protéine RGS7, et ils formeraient ainsi avec GPR158 un complexe de régulation de l'activité du récepteur orphelin ainsi que d'autres RCPG présents dans le nano-environnement de GPR158. Enfin, afin de mieux comprendre la fonction et les possibles voies de signalisation de GPR158, une analyse protéomique des complexes multi-protéiques bâtis autour du domaine C-ter de GPR158, a été menée. Après purification du récepteur orphelin et des protéines associées par immunoprécipitation, l'identification par spectrométrie de masse des protéines présentes a permis d'identifier 6 nouveaux partenaires potentiels. Parmi eux, quatre protéines, p53, PPM1G, Sgt1 et SIRT1, sont des régulateurs du facteur de transcription suppresseur de tumeur p53, et deux protéines, SIRT1 et TRIM58, sont impliquées dans le processus de vieillissement cellulaire. Par conséquent, une implication dans la transcription, la régulation du cycle cellulaire, la réparation de l'ADN, la prolifération, l'apoptose, la tumorigenèse et le vieillissement, du récepteur orphelin GPR158 peut être envisagée. / G protein-coupled receptors (GPCR) are known to form the largest family of cell communication proteins, and to participate to all functions of the body, making them high potential therapeutic targets. However, lots of these proteins are still orphan receptors, for which no ligand, neither function have been described, although some could be of very high interest, like GPR158, a class C orphan GPCR. The seven transmembrane domain (7TM) of this orphan receptor was related to class C GPCR (GPR158 and GABAB share 20% sequence identity in the TM core region) but its N-terminal domain was not homologous to the typical Venus Flytrap (VFT) known to bind the ligands in most of class C receptors. Which suggests that GPR158 has developed different ligand binding mode. GPR158 is expressed mainly in the brain. Interestingly, the expression of this receptor has been found in many cells and tissues to be potentially regulated in pathological conditions, of which 50% are cancerous diseases. We thus intended to decipher its cellular function and partners, to understand its potential physiological and physiopathological roles. Initially, our goal was to determine the functionality of GPR158, and the possible signaling and cellular mechanisms it was involved in, by looking for some constitutive activity for this orphan GPCR, in the absensce of any ligand. Curiously, we could not detect any G protein coupling, like constitutive G protein stimulation by overexpression of wild type, mutated, truncated and chimeric receptors. This despite the residues of intracellular loops and TM domain, important for the G protein coupling and for the activation of other GPCR, which are conserved in GPR158. This suggests that GPR158 in itself might not have a signalization, and thus it would regulate the activity of other GPCR. Alternatively, GPR158 would have an original way of signaling to be discovered with more sophisticated techniques.Then, we tried to understand the role of three VCPWE specific motifs that we have identified at the long C-terminal (C-ter) domain of GPR158. These motifs are well conserved among different species and thus would play important functional roles. Therefore, we have shown that the third motif indeed binds G protein alpha o subunit, likely in active state. Interestingly, we have also shown that RGS7 that deactivated alpha o, interacts constitutively with the C-terminal domain of GPR158 upstream of VCPWE motifs. Thus, RGS7 would regulate the alpha subunit association with GPR158. Hence, GPR158 would act as a signaling regulatory platform, controlling G protein pathways by binding active alpha subunit and RGS7. This would be of great importance as a local signaling regulatory mechanism. Finally, to better understand the function and possible signaling pathways of GPR158, a proteomic analysis of multi-protein complexes built around the C-ter domain of GPR158, was conducted. After purification of the orphan receptor and its associated proteins by immunoprecipitation, the identification by mass spectrometry of GPR158 interacting proteins led to the identification of six potential new partners. Among them, four proteins, p53, PPM1G, SGT1 and SIRT1, are regulators of the p53 tumor suppressor protein widely known for its role as a transcription factor that regulates the expression of stress response genes, and two proteins, SIRT1 and TRIM58 are involved in cellular aging process. Therefore, GPR158 could be involved in transcription, cell cycle regulation, DNA repair, proliferation, apoptosis, tumorigenesis and cell aging.