Prof. Dr. Sebastian Hiller Department Biozentrum Profiles & Affiliations OverviewResearch Publications Projects & Collaborations Projects & Collaborations OverviewResearch Publications Projects & Collaborations Profiles & Affiliations Projects & Collaborations 29 foundShow per page10 10 20 50 Design of antimicrobial peptides through active learning Research Project | 2 Project MembersNo Description available Protein-protein interaction antagonists Research Project | 1 Project MembersNo Description available EMBO Fellowship for Patrick Fischer Research Project | 1 Project MembersEMBO Fellowship for Patrick Fischer Efficient Characterization of Biomolecular Interactions by Automated Isothermal Titration Calorimetry Research Project | 5 Project MembersInhalt und Ziel des Forschungsprojekts Im Gegensatz zu anderen Methoden ist die isothermale Titrationskalorimetrie (ITC) in einzigartiger Weise geeignet, die Wechselwirkung von unmodifizierten Bindungspartnern anhand der aufgenommenen oder abgegebenen Bindungswärme zu messen. Messungen mittels ITC erlauben dabei eine thermodynamische Charakterisierung der Wechselwirkungen zwischen Bindungspartnern. Diese erlaubt, zusammen mit Strukturinformationen, die Mechanismen der Bindung im Detail zu verstehen und zu erklären, warum verschiedene Bindungspartner unterschiedlich stark interagieren. In diesem Projekt wird ein automatisiertes System für ITC Messungen aufgebaut, das hilft, wesentliche Nachteile von manuellen Messungen hinsichtlich des Durchsatzes und der Datenqualität zu überkommen. Das neue ITC System wird in der Biophysik Forschungsserviceeinheit (BF) des Biozentrums der Universität Basel installiert und betrieben, und steht dort auch externen Nutzern zur Verfügung. Erste Anwendungen des neuen Geräts sind in den Bereichen Antibiotikaentwicklung und Antibiotikaresistenzen, sowie der molekularen und zellulären Krebsforschung vorgesehen. Wissenschaftlicher und gesellschaftlicher Kontext Wir erwarten, dass dieses Projekt zu einem besseren Verständnis fundamentaler biologischer Prozesse beitragen wird und dass die entsprechenden Erkenntnisse einen wertvollen Beitrag zu der Entwicklung von Molekülen leisten, die als Werkzeuge in der Biologie oder als Vorstufen zukünftiger Medikamente dienen. Structure and mechanism of Leptospira's virulence switch Research Project | 1 Project MembersStructure and mechanism of Leptospira's virulence switch Mechanistic dynamics of the chaperone network in the endoplasmatic reticulum Research Project | 1 Project MembersMechanistic dynamics of the chaperone network in the endoplasmatic reticulum Structure-function analysis of the RNA-binding protein PGC-1a in skeletal muscle Research Project | 2 Project MembersPlasticity of cells, tissues and organs relies on sensing of external and internal cues, integration of the engaged signaling pathways, and orchestration of a pleiotropic response. For example, contractile patterns, ambient temperature and oxygen levels, nutrient availability and composition, as well as other factors result in a massive remodeling of biochemical pathways, cellular metabolism and mechanical properties of skeletal muscle cells, most notably in the context of repeated bouts of exercise, ultimately leading to training adaptations. In turn, such adaptations of skeletal muscle trigger internal and external changes that contribute to the systemic effects of exercise with many health benefits, and strong preventative and therapeutic outcomes in a number of pathologies. Surprisingly, even though the physiological and clinical contributions of exercise-linked muscle plasticity are well recognized, the molecular mechanisms that control the corresponding biological programs are still poorly understood. In recent years, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has emerged as a central regulatory nexus of plasticity in various cell types. PGC-1α integrates upstream signaling pathways to coordinate the complex transcriptional networks encoding biological programs involved in mitochondrial function, cellular metabolism and more. In the case of endurance exercise-mediated plasticity of muscle cells, most, if not all of the adaptations are evoked by this stimulus. Accordingly, muscle-specific overexpression or knockout of PGC-1α elicits high endurance and pathologically sedentary phenotypes, respectively. Our proposal aims at elucidating the molecular underpinnings of the complex transcriptional control that is exerted by PGC-1α in a spatio-temporal manner. We have recently discovered that the binding of RNAs to PGC-1α contributes to full transcriptional activity, and is central for the inclusion of PGC-1α-containing multiprotein complexes in liquid-liquid phase separated nuclear condensates for the sequestration of transcription. We now plan to determine the list and common features of PGC-1α-bound RNAs, interrogate how RNA binding is brought about in a structure-function analysis, study the consequences on multiprotein complex formation, and ultimately investigate the physiological relevance in skeletal muscle cells in vitro and in vivo . To do so, novel animal models will be leveraged for single-end enhanced crosslinking and immunoprecipitation (seCLIP) experiments to identify PGC-1α-bound RNAs, structural information will be obtained by NMR spectroscopy, and validated using site-directed mutagenesis of key amino acids and nucleotides in PGC-1α and RNAs, respectively, to study PGC-1α-dependent liquid-liquid phase separation. Then, PGC-1α-containing multiprotein complexes will be co-purified to perform cryo-electron microscopy-based single particle structural analysis. Finally, the functional consequence of targeted mutagenesis of key residues will be assessed in muscle cells in culture and mouse muscle in vivo with state-of-the-art myotropic adeno-associated viral vectors (AAVMYO). The research plan thus a.) highly synergizes in terms of interdisciplinary approaches between the groups involved and b.) will result in hitherto unprecedented insights into molecular mechanisms that underlie complex spatio-temporal control of transcriptional networks with important implications for the understanding of cellular and tissue plasticity in health and disease. Bacterial Type IV Secretion (T4S): Cellular, Molecular and Evolutionary Basis of the Subversion of Host Cell Functions by Translocated Effector Proteins Research Project | 2 Project MembersIn the ongoing funding period of SNSF grant 31003A-173119 we are studying the cellular, molecular and evolutionary basis of subversion of host cell functions by type IV secretion (T4S) effector proteins during chronic bacterial infection by the related zoonotic pathogens Bartonella and Brucella. The three-year pro rata temporis extension in the frame of the excellence grant will allow us to extend our studies towards a better understanding (i) of the evolutionary origin and function of these host cell-targeted effector proteins and (ii) of the nature of their signal for T4S-dependent translocation. In Subproject A we will continue the functional characterization of Bartonella effector proteins (Beps) translocated by the VirB T4S system and the structure/function analysis of the BID domain as principle constituent of their T4S signal. Furthermore, we will extend our multidisciplinary studies to an unrelated class of newly identified T4S effectors in Bartonella with homology to a family of widespread type III secretion (T3S) effectors. Furthermore, we will study the role of the Bartonella Gene Transfer Agent (BaGTA) in facilitating adaptive evolution of Beps and associated virulence factors in processes like host adaptation. Subproject B will focus on the functional analysis of effector proteins translocated by the distinct VirB T4S system of Brucella with particular emphasis on delineating the unknown T4S signal. Together, these studies will contribute fundamentally to our molecular understanding of the widespread T4S mechanism in the context of chronic bacterial infections. NCCR AntiResist: New approaches to combat antibiotic-resistant bacteria Umbrella Project | 32 Project MembersAntibiotics are powerful and indispensable drugs to treat life threatening bacterial infections such as sepsis or pneumonia. Antibiotics also play a central role in many other areas of modern medicine, in particular to protect patients with compromised immunity during cancer therapies, transplantations or surgical interventions. These achievements are now at risk, with the fraction of bacterial pathogens that are resistant to one or more antibiotics steadily increasing. In addition, development of novel antimicrobials lags behind, suffering from inherently high attrition rates in particular for drug candidates against the most problematic Gram-negative bacteria. Together, these factors increasingly limit the options clinicians have for treating bacterial infections. The overarching goal of NCCR AntiResist is to elucidate the physiological properties of bacterial pathogens in infected human patients in order to find new ways of combatting superbugs. Among the many societal, economic, and scientific factors that impact on the development of alternative strategies for antibiotic discovery, our limited understanding of the physiology and heterogeneity of bacterial pathogens in patients ranks highly. Bacteria growing in tissues of patients experience environments very different from standard laboratory conditions, resulting in radically different microbial physiology and population heterogeneity compared to conditions generally used for antibacterial discovery. There is currently no systematic strategy to overcome this fundamental problem. This has resulted in: (i) suboptimal screens that identify new antibiotics, which do not target the special properties of bacteria growing within the patient; (ii) an inability to properly evaluate the efficacy of non-conventional antibacterial strategies; (iii) missed opportunities for entirely new treatment strategies. This NCCR utilizes patient samples from ongoing clinical studies and establishes a unique multidisciplinary network of clinicians, biologists, engineers, chemists, computational scientists and drug developers that will overcome this problem. We are excited to merge these disciplines in order to determine the properties of pathogens infecting patients, establish conditions in the lab that reproduce these properties and utilize these in-vitro models for antimicrobial discovery and development. In addition, clinical-trial networks and the pharmaceutical industry have major footprints in antimicrobial R&D. Exploiting synergies between these players has great potential for making transformative progress in this critical field of human health. This NCCR maintains active collaborations with Biotech SMEs and large pharmaceutical companies with the goal to: accelerate antibiotic discovery by providing relevant read-outs for early prioritization of compounds; enable innovative screens for non-canonical strategies such as anti-virulence inhibitors and immunomodulators; identify new antibacterial strategies that effectively combat bacteria either by targeting refractory subpopulations or by synergizing with bacterial stresses imposed by the patients' own immune system. This NCCR proposes a paradigm shift in antibiotic discovery by investigating the physiology of bacterial pathogens in human patients. This knowledge will be used to develop assays for molecular analyses and drug screening under relevant conditions and to accelerate antibacterial discovery, improve treatment regimens, and uncover novel targets for eradicating pathogens. Through this concerted effort, this NCCR will make a crucial and unique contribution to winning the race against superbugs. Development of NLRP3-ASC selective inhibitors Research Project | 1 Project MembersDuring an attack from pathogens organisms produce inflammatory cytokines, such as IL-1β and IL-18, that act to combat infection. However, prolonged and uncontrolled production of inflammatory cytokines, usually due to sterile inflammatory triggers, causes chronic inflammation. The latter is the underlying cause of several (auto)-inflammatory diseases such as gout, CAPS (Cryopyrin-Associated Periodic Syndromes), arthritis, Alzheimer's disease, etc. The main cellular node activated by sterile (auto)-inflammatory triggers is NLRP3-inflammasome (NACHT, LRR and PYD domains-containing protein 3). Main drugs against chronic inflammation act downstream of the NLRP3-inflammasome by targeting the release of inflammatory cytokines, with variable efficacity. However, these drugs block the entire inflammatory response, as such, an increase in the rate of infections is a main concern. Alternatively, blocking specifically the NLRP3-inflammasome would inhibit only one branch of the innate immune response having an immense potential to treat (auto)-inflammatory disorders with fewer side effects. As of today, there are no NLRP3-inflamasome targeting drugs on the market. To develop such an inhibitor, we are focusing on 11 small molecules obtained from a cell-based screen of over 10'000 compounds. Our small molecules have novel chemistry to the known NLRP3 inhibitors and, without optimization, show NLRP3-inflammasome inhibitor activity comparable to known NLRP3 inhibitors. During the course of this feasibility study, we will perform hit-to-lead optimization and find the molecular mechanism of action of our compounds. We aim for a business-to-business model. By combining the expertise of our team in structural biology, immunology, organic chemistry and animal experimentation we will generate intellectual property that we can patent, and use as leverage to find business partners to push our compounds towards Phase I clinical trials. 123 123 OverviewResearch Publications Projects & Collaborations
Projects & Collaborations 29 foundShow per page10 10 20 50 Design of antimicrobial peptides through active learning Research Project | 2 Project MembersNo Description available Protein-protein interaction antagonists Research Project | 1 Project MembersNo Description available EMBO Fellowship for Patrick Fischer Research Project | 1 Project MembersEMBO Fellowship for Patrick Fischer Efficient Characterization of Biomolecular Interactions by Automated Isothermal Titration Calorimetry Research Project | 5 Project MembersInhalt und Ziel des Forschungsprojekts Im Gegensatz zu anderen Methoden ist die isothermale Titrationskalorimetrie (ITC) in einzigartiger Weise geeignet, die Wechselwirkung von unmodifizierten Bindungspartnern anhand der aufgenommenen oder abgegebenen Bindungswärme zu messen. Messungen mittels ITC erlauben dabei eine thermodynamische Charakterisierung der Wechselwirkungen zwischen Bindungspartnern. Diese erlaubt, zusammen mit Strukturinformationen, die Mechanismen der Bindung im Detail zu verstehen und zu erklären, warum verschiedene Bindungspartner unterschiedlich stark interagieren. In diesem Projekt wird ein automatisiertes System für ITC Messungen aufgebaut, das hilft, wesentliche Nachteile von manuellen Messungen hinsichtlich des Durchsatzes und der Datenqualität zu überkommen. Das neue ITC System wird in der Biophysik Forschungsserviceeinheit (BF) des Biozentrums der Universität Basel installiert und betrieben, und steht dort auch externen Nutzern zur Verfügung. Erste Anwendungen des neuen Geräts sind in den Bereichen Antibiotikaentwicklung und Antibiotikaresistenzen, sowie der molekularen und zellulären Krebsforschung vorgesehen. Wissenschaftlicher und gesellschaftlicher Kontext Wir erwarten, dass dieses Projekt zu einem besseren Verständnis fundamentaler biologischer Prozesse beitragen wird und dass die entsprechenden Erkenntnisse einen wertvollen Beitrag zu der Entwicklung von Molekülen leisten, die als Werkzeuge in der Biologie oder als Vorstufen zukünftiger Medikamente dienen. Structure and mechanism of Leptospira's virulence switch Research Project | 1 Project MembersStructure and mechanism of Leptospira's virulence switch Mechanistic dynamics of the chaperone network in the endoplasmatic reticulum Research Project | 1 Project MembersMechanistic dynamics of the chaperone network in the endoplasmatic reticulum Structure-function analysis of the RNA-binding protein PGC-1a in skeletal muscle Research Project | 2 Project MembersPlasticity of cells, tissues and organs relies on sensing of external and internal cues, integration of the engaged signaling pathways, and orchestration of a pleiotropic response. For example, contractile patterns, ambient temperature and oxygen levels, nutrient availability and composition, as well as other factors result in a massive remodeling of biochemical pathways, cellular metabolism and mechanical properties of skeletal muscle cells, most notably in the context of repeated bouts of exercise, ultimately leading to training adaptations. In turn, such adaptations of skeletal muscle trigger internal and external changes that contribute to the systemic effects of exercise with many health benefits, and strong preventative and therapeutic outcomes in a number of pathologies. Surprisingly, even though the physiological and clinical contributions of exercise-linked muscle plasticity are well recognized, the molecular mechanisms that control the corresponding biological programs are still poorly understood. In recent years, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has emerged as a central regulatory nexus of plasticity in various cell types. PGC-1α integrates upstream signaling pathways to coordinate the complex transcriptional networks encoding biological programs involved in mitochondrial function, cellular metabolism and more. In the case of endurance exercise-mediated plasticity of muscle cells, most, if not all of the adaptations are evoked by this stimulus. Accordingly, muscle-specific overexpression or knockout of PGC-1α elicits high endurance and pathologically sedentary phenotypes, respectively. Our proposal aims at elucidating the molecular underpinnings of the complex transcriptional control that is exerted by PGC-1α in a spatio-temporal manner. We have recently discovered that the binding of RNAs to PGC-1α contributes to full transcriptional activity, and is central for the inclusion of PGC-1α-containing multiprotein complexes in liquid-liquid phase separated nuclear condensates for the sequestration of transcription. We now plan to determine the list and common features of PGC-1α-bound RNAs, interrogate how RNA binding is brought about in a structure-function analysis, study the consequences on multiprotein complex formation, and ultimately investigate the physiological relevance in skeletal muscle cells in vitro and in vivo . To do so, novel animal models will be leveraged for single-end enhanced crosslinking and immunoprecipitation (seCLIP) experiments to identify PGC-1α-bound RNAs, structural information will be obtained by NMR spectroscopy, and validated using site-directed mutagenesis of key amino acids and nucleotides in PGC-1α and RNAs, respectively, to study PGC-1α-dependent liquid-liquid phase separation. Then, PGC-1α-containing multiprotein complexes will be co-purified to perform cryo-electron microscopy-based single particle structural analysis. Finally, the functional consequence of targeted mutagenesis of key residues will be assessed in muscle cells in culture and mouse muscle in vivo with state-of-the-art myotropic adeno-associated viral vectors (AAVMYO). The research plan thus a.) highly synergizes in terms of interdisciplinary approaches between the groups involved and b.) will result in hitherto unprecedented insights into molecular mechanisms that underlie complex spatio-temporal control of transcriptional networks with important implications for the understanding of cellular and tissue plasticity in health and disease. Bacterial Type IV Secretion (T4S): Cellular, Molecular and Evolutionary Basis of the Subversion of Host Cell Functions by Translocated Effector Proteins Research Project | 2 Project MembersIn the ongoing funding period of SNSF grant 31003A-173119 we are studying the cellular, molecular and evolutionary basis of subversion of host cell functions by type IV secretion (T4S) effector proteins during chronic bacterial infection by the related zoonotic pathogens Bartonella and Brucella. The three-year pro rata temporis extension in the frame of the excellence grant will allow us to extend our studies towards a better understanding (i) of the evolutionary origin and function of these host cell-targeted effector proteins and (ii) of the nature of their signal for T4S-dependent translocation. In Subproject A we will continue the functional characterization of Bartonella effector proteins (Beps) translocated by the VirB T4S system and the structure/function analysis of the BID domain as principle constituent of their T4S signal. Furthermore, we will extend our multidisciplinary studies to an unrelated class of newly identified T4S effectors in Bartonella with homology to a family of widespread type III secretion (T3S) effectors. Furthermore, we will study the role of the Bartonella Gene Transfer Agent (BaGTA) in facilitating adaptive evolution of Beps and associated virulence factors in processes like host adaptation. Subproject B will focus on the functional analysis of effector proteins translocated by the distinct VirB T4S system of Brucella with particular emphasis on delineating the unknown T4S signal. Together, these studies will contribute fundamentally to our molecular understanding of the widespread T4S mechanism in the context of chronic bacterial infections. NCCR AntiResist: New approaches to combat antibiotic-resistant bacteria Umbrella Project | 32 Project MembersAntibiotics are powerful and indispensable drugs to treat life threatening bacterial infections such as sepsis or pneumonia. Antibiotics also play a central role in many other areas of modern medicine, in particular to protect patients with compromised immunity during cancer therapies, transplantations or surgical interventions. These achievements are now at risk, with the fraction of bacterial pathogens that are resistant to one or more antibiotics steadily increasing. In addition, development of novel antimicrobials lags behind, suffering from inherently high attrition rates in particular for drug candidates against the most problematic Gram-negative bacteria. Together, these factors increasingly limit the options clinicians have for treating bacterial infections. The overarching goal of NCCR AntiResist is to elucidate the physiological properties of bacterial pathogens in infected human patients in order to find new ways of combatting superbugs. Among the many societal, economic, and scientific factors that impact on the development of alternative strategies for antibiotic discovery, our limited understanding of the physiology and heterogeneity of bacterial pathogens in patients ranks highly. Bacteria growing in tissues of patients experience environments very different from standard laboratory conditions, resulting in radically different microbial physiology and population heterogeneity compared to conditions generally used for antibacterial discovery. There is currently no systematic strategy to overcome this fundamental problem. This has resulted in: (i) suboptimal screens that identify new antibiotics, which do not target the special properties of bacteria growing within the patient; (ii) an inability to properly evaluate the efficacy of non-conventional antibacterial strategies; (iii) missed opportunities for entirely new treatment strategies. This NCCR utilizes patient samples from ongoing clinical studies and establishes a unique multidisciplinary network of clinicians, biologists, engineers, chemists, computational scientists and drug developers that will overcome this problem. We are excited to merge these disciplines in order to determine the properties of pathogens infecting patients, establish conditions in the lab that reproduce these properties and utilize these in-vitro models for antimicrobial discovery and development. In addition, clinical-trial networks and the pharmaceutical industry have major footprints in antimicrobial R&D. Exploiting synergies between these players has great potential for making transformative progress in this critical field of human health. This NCCR maintains active collaborations with Biotech SMEs and large pharmaceutical companies with the goal to: accelerate antibiotic discovery by providing relevant read-outs for early prioritization of compounds; enable innovative screens for non-canonical strategies such as anti-virulence inhibitors and immunomodulators; identify new antibacterial strategies that effectively combat bacteria either by targeting refractory subpopulations or by synergizing with bacterial stresses imposed by the patients' own immune system. This NCCR proposes a paradigm shift in antibiotic discovery by investigating the physiology of bacterial pathogens in human patients. This knowledge will be used to develop assays for molecular analyses and drug screening under relevant conditions and to accelerate antibacterial discovery, improve treatment regimens, and uncover novel targets for eradicating pathogens. Through this concerted effort, this NCCR will make a crucial and unique contribution to winning the race against superbugs. Development of NLRP3-ASC selective inhibitors Research Project | 1 Project MembersDuring an attack from pathogens organisms produce inflammatory cytokines, such as IL-1β and IL-18, that act to combat infection. However, prolonged and uncontrolled production of inflammatory cytokines, usually due to sterile inflammatory triggers, causes chronic inflammation. The latter is the underlying cause of several (auto)-inflammatory diseases such as gout, CAPS (Cryopyrin-Associated Periodic Syndromes), arthritis, Alzheimer's disease, etc. The main cellular node activated by sterile (auto)-inflammatory triggers is NLRP3-inflammasome (NACHT, LRR and PYD domains-containing protein 3). Main drugs against chronic inflammation act downstream of the NLRP3-inflammasome by targeting the release of inflammatory cytokines, with variable efficacity. However, these drugs block the entire inflammatory response, as such, an increase in the rate of infections is a main concern. Alternatively, blocking specifically the NLRP3-inflammasome would inhibit only one branch of the innate immune response having an immense potential to treat (auto)-inflammatory disorders with fewer side effects. As of today, there are no NLRP3-inflamasome targeting drugs on the market. To develop such an inhibitor, we are focusing on 11 small molecules obtained from a cell-based screen of over 10'000 compounds. Our small molecules have novel chemistry to the known NLRP3 inhibitors and, without optimization, show NLRP3-inflammasome inhibitor activity comparable to known NLRP3 inhibitors. During the course of this feasibility study, we will perform hit-to-lead optimization and find the molecular mechanism of action of our compounds. We aim for a business-to-business model. By combining the expertise of our team in structural biology, immunology, organic chemistry and animal experimentation we will generate intellectual property that we can patent, and use as leverage to find business partners to push our compounds towards Phase I clinical trials. 123 123
Design of antimicrobial peptides through active learning Research Project | 2 Project MembersNo Description available
EMBO Fellowship for Patrick Fischer Research Project | 1 Project MembersEMBO Fellowship for Patrick Fischer
Efficient Characterization of Biomolecular Interactions by Automated Isothermal Titration Calorimetry Research Project | 5 Project MembersInhalt und Ziel des Forschungsprojekts Im Gegensatz zu anderen Methoden ist die isothermale Titrationskalorimetrie (ITC) in einzigartiger Weise geeignet, die Wechselwirkung von unmodifizierten Bindungspartnern anhand der aufgenommenen oder abgegebenen Bindungswärme zu messen. Messungen mittels ITC erlauben dabei eine thermodynamische Charakterisierung der Wechselwirkungen zwischen Bindungspartnern. Diese erlaubt, zusammen mit Strukturinformationen, die Mechanismen der Bindung im Detail zu verstehen und zu erklären, warum verschiedene Bindungspartner unterschiedlich stark interagieren. In diesem Projekt wird ein automatisiertes System für ITC Messungen aufgebaut, das hilft, wesentliche Nachteile von manuellen Messungen hinsichtlich des Durchsatzes und der Datenqualität zu überkommen. Das neue ITC System wird in der Biophysik Forschungsserviceeinheit (BF) des Biozentrums der Universität Basel installiert und betrieben, und steht dort auch externen Nutzern zur Verfügung. Erste Anwendungen des neuen Geräts sind in den Bereichen Antibiotikaentwicklung und Antibiotikaresistenzen, sowie der molekularen und zellulären Krebsforschung vorgesehen. Wissenschaftlicher und gesellschaftlicher Kontext Wir erwarten, dass dieses Projekt zu einem besseren Verständnis fundamentaler biologischer Prozesse beitragen wird und dass die entsprechenden Erkenntnisse einen wertvollen Beitrag zu der Entwicklung von Molekülen leisten, die als Werkzeuge in der Biologie oder als Vorstufen zukünftiger Medikamente dienen.
Structure and mechanism of Leptospira's virulence switch Research Project | 1 Project MembersStructure and mechanism of Leptospira's virulence switch
Mechanistic dynamics of the chaperone network in the endoplasmatic reticulum Research Project | 1 Project MembersMechanistic dynamics of the chaperone network in the endoplasmatic reticulum
Structure-function analysis of the RNA-binding protein PGC-1a in skeletal muscle Research Project | 2 Project MembersPlasticity of cells, tissues and organs relies on sensing of external and internal cues, integration of the engaged signaling pathways, and orchestration of a pleiotropic response. For example, contractile patterns, ambient temperature and oxygen levels, nutrient availability and composition, as well as other factors result in a massive remodeling of biochemical pathways, cellular metabolism and mechanical properties of skeletal muscle cells, most notably in the context of repeated bouts of exercise, ultimately leading to training adaptations. In turn, such adaptations of skeletal muscle trigger internal and external changes that contribute to the systemic effects of exercise with many health benefits, and strong preventative and therapeutic outcomes in a number of pathologies. Surprisingly, even though the physiological and clinical contributions of exercise-linked muscle plasticity are well recognized, the molecular mechanisms that control the corresponding biological programs are still poorly understood. In recent years, the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α) has emerged as a central regulatory nexus of plasticity in various cell types. PGC-1α integrates upstream signaling pathways to coordinate the complex transcriptional networks encoding biological programs involved in mitochondrial function, cellular metabolism and more. In the case of endurance exercise-mediated plasticity of muscle cells, most, if not all of the adaptations are evoked by this stimulus. Accordingly, muscle-specific overexpression or knockout of PGC-1α elicits high endurance and pathologically sedentary phenotypes, respectively. Our proposal aims at elucidating the molecular underpinnings of the complex transcriptional control that is exerted by PGC-1α in a spatio-temporal manner. We have recently discovered that the binding of RNAs to PGC-1α contributes to full transcriptional activity, and is central for the inclusion of PGC-1α-containing multiprotein complexes in liquid-liquid phase separated nuclear condensates for the sequestration of transcription. We now plan to determine the list and common features of PGC-1α-bound RNAs, interrogate how RNA binding is brought about in a structure-function analysis, study the consequences on multiprotein complex formation, and ultimately investigate the physiological relevance in skeletal muscle cells in vitro and in vivo . To do so, novel animal models will be leveraged for single-end enhanced crosslinking and immunoprecipitation (seCLIP) experiments to identify PGC-1α-bound RNAs, structural information will be obtained by NMR spectroscopy, and validated using site-directed mutagenesis of key amino acids and nucleotides in PGC-1α and RNAs, respectively, to study PGC-1α-dependent liquid-liquid phase separation. Then, PGC-1α-containing multiprotein complexes will be co-purified to perform cryo-electron microscopy-based single particle structural analysis. Finally, the functional consequence of targeted mutagenesis of key residues will be assessed in muscle cells in culture and mouse muscle in vivo with state-of-the-art myotropic adeno-associated viral vectors (AAVMYO). The research plan thus a.) highly synergizes in terms of interdisciplinary approaches between the groups involved and b.) will result in hitherto unprecedented insights into molecular mechanisms that underlie complex spatio-temporal control of transcriptional networks with important implications for the understanding of cellular and tissue plasticity in health and disease.
Bacterial Type IV Secretion (T4S): Cellular, Molecular and Evolutionary Basis of the Subversion of Host Cell Functions by Translocated Effector Proteins Research Project | 2 Project MembersIn the ongoing funding period of SNSF grant 31003A-173119 we are studying the cellular, molecular and evolutionary basis of subversion of host cell functions by type IV secretion (T4S) effector proteins during chronic bacterial infection by the related zoonotic pathogens Bartonella and Brucella. The three-year pro rata temporis extension in the frame of the excellence grant will allow us to extend our studies towards a better understanding (i) of the evolutionary origin and function of these host cell-targeted effector proteins and (ii) of the nature of their signal for T4S-dependent translocation. In Subproject A we will continue the functional characterization of Bartonella effector proteins (Beps) translocated by the VirB T4S system and the structure/function analysis of the BID domain as principle constituent of their T4S signal. Furthermore, we will extend our multidisciplinary studies to an unrelated class of newly identified T4S effectors in Bartonella with homology to a family of widespread type III secretion (T3S) effectors. Furthermore, we will study the role of the Bartonella Gene Transfer Agent (BaGTA) in facilitating adaptive evolution of Beps and associated virulence factors in processes like host adaptation. Subproject B will focus on the functional analysis of effector proteins translocated by the distinct VirB T4S system of Brucella with particular emphasis on delineating the unknown T4S signal. Together, these studies will contribute fundamentally to our molecular understanding of the widespread T4S mechanism in the context of chronic bacterial infections.
NCCR AntiResist: New approaches to combat antibiotic-resistant bacteria Umbrella Project | 32 Project MembersAntibiotics are powerful and indispensable drugs to treat life threatening bacterial infections such as sepsis or pneumonia. Antibiotics also play a central role in many other areas of modern medicine, in particular to protect patients with compromised immunity during cancer therapies, transplantations or surgical interventions. These achievements are now at risk, with the fraction of bacterial pathogens that are resistant to one or more antibiotics steadily increasing. In addition, development of novel antimicrobials lags behind, suffering from inherently high attrition rates in particular for drug candidates against the most problematic Gram-negative bacteria. Together, these factors increasingly limit the options clinicians have for treating bacterial infections. The overarching goal of NCCR AntiResist is to elucidate the physiological properties of bacterial pathogens in infected human patients in order to find new ways of combatting superbugs. Among the many societal, economic, and scientific factors that impact on the development of alternative strategies for antibiotic discovery, our limited understanding of the physiology and heterogeneity of bacterial pathogens in patients ranks highly. Bacteria growing in tissues of patients experience environments very different from standard laboratory conditions, resulting in radically different microbial physiology and population heterogeneity compared to conditions generally used for antibacterial discovery. There is currently no systematic strategy to overcome this fundamental problem. This has resulted in: (i) suboptimal screens that identify new antibiotics, which do not target the special properties of bacteria growing within the patient; (ii) an inability to properly evaluate the efficacy of non-conventional antibacterial strategies; (iii) missed opportunities for entirely new treatment strategies. This NCCR utilizes patient samples from ongoing clinical studies and establishes a unique multidisciplinary network of clinicians, biologists, engineers, chemists, computational scientists and drug developers that will overcome this problem. We are excited to merge these disciplines in order to determine the properties of pathogens infecting patients, establish conditions in the lab that reproduce these properties and utilize these in-vitro models for antimicrobial discovery and development. In addition, clinical-trial networks and the pharmaceutical industry have major footprints in antimicrobial R&D. Exploiting synergies between these players has great potential for making transformative progress in this critical field of human health. This NCCR maintains active collaborations with Biotech SMEs and large pharmaceutical companies with the goal to: accelerate antibiotic discovery by providing relevant read-outs for early prioritization of compounds; enable innovative screens for non-canonical strategies such as anti-virulence inhibitors and immunomodulators; identify new antibacterial strategies that effectively combat bacteria either by targeting refractory subpopulations or by synergizing with bacterial stresses imposed by the patients' own immune system. This NCCR proposes a paradigm shift in antibiotic discovery by investigating the physiology of bacterial pathogens in human patients. This knowledge will be used to develop assays for molecular analyses and drug screening under relevant conditions and to accelerate antibacterial discovery, improve treatment regimens, and uncover novel targets for eradicating pathogens. Through this concerted effort, this NCCR will make a crucial and unique contribution to winning the race against superbugs.
Development of NLRP3-ASC selective inhibitors Research Project | 1 Project MembersDuring an attack from pathogens organisms produce inflammatory cytokines, such as IL-1β and IL-18, that act to combat infection. However, prolonged and uncontrolled production of inflammatory cytokines, usually due to sterile inflammatory triggers, causes chronic inflammation. The latter is the underlying cause of several (auto)-inflammatory diseases such as gout, CAPS (Cryopyrin-Associated Periodic Syndromes), arthritis, Alzheimer's disease, etc. The main cellular node activated by sterile (auto)-inflammatory triggers is NLRP3-inflammasome (NACHT, LRR and PYD domains-containing protein 3). Main drugs against chronic inflammation act downstream of the NLRP3-inflammasome by targeting the release of inflammatory cytokines, with variable efficacity. However, these drugs block the entire inflammatory response, as such, an increase in the rate of infections is a main concern. Alternatively, blocking specifically the NLRP3-inflammasome would inhibit only one branch of the innate immune response having an immense potential to treat (auto)-inflammatory disorders with fewer side effects. As of today, there are no NLRP3-inflamasome targeting drugs on the market. To develop such an inhibitor, we are focusing on 11 small molecules obtained from a cell-based screen of over 10'000 compounds. Our small molecules have novel chemistry to the known NLRP3 inhibitors and, without optimization, show NLRP3-inflammasome inhibitor activity comparable to known NLRP3 inhibitors. During the course of this feasibility study, we will perform hit-to-lead optimization and find the molecular mechanism of action of our compounds. We aim for a business-to-business model. By combining the expertise of our team in structural biology, immunology, organic chemistry and animal experimentation we will generate intellectual property that we can patent, and use as leverage to find business partners to push our compounds towards Phase I clinical trials.
