23 results on '"Barillari C"'
Search Results
2. Making the Difference in Occupational Health: Three Original and Significant Cases Presented at ICOH Congresses in the 20th Century
- Author
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Iavicoli, S, Valenti, A, Barillari, C, Fortuna, G, Boccuni, V, Carnevale, F, Riva, M, Kang, S, Tomassini, L, Iavicoli, Sergio, Valenti, Antonio, Barillari, Caterina, Fortuna, Grazia, Boccuni, Valeria, Carnevale, Francesco, Riva, Michele A., Kang, Seong-Kyu, Tomassini, Luigi, Iavicoli, S, Valenti, A, Barillari, C, Fortuna, G, Boccuni, V, Carnevale, F, Riva, M, Kang, S, Tomassini, L, Iavicoli, Sergio, Valenti, Antonio, Barillari, Caterina, Fortuna, Grazia, Boccuni, Valeria, Carnevale, Francesco, Riva, Michele A., Kang, Seong-Kyu, and Tomassini, Luigi
- Abstract
Background The aim of this study is to illustrate the historical role of the International Commission on Occupational Health (ICOH) congresses as an arena where national and international occupational medicine can dialogue and as the first example of scientific transferability of the research and prevention results that have had such an impact on global public health. Methods We used the ICOH Heritage Repository, in which ICOH congress proceedings (from the first congress in Milan in 1906 to the last congress, held in Dublin in 2018), are organised in an orderly way, updated and easily accessible according to open access logic. Results We describe studies by three physicians who submitted significant scientific work to ICOH congresses, one on the battle against ancylostomiasis (Volante, 1906), the second (Quarelli, 1928) on carbon disulphide poisoning, and the third (Viola, 1969) on the carcinogenicity of vinyl chloride monomer. Priority is given to Italian cases, on account of the authors’ obvious familiarity with the issues. Conclusion The visibility offered in ICOH conferences and their published proceedings has boosted the international spread of their findings, contributing to the scientific transferability of the research results and influencing the development of policies and prevention interventions that have had a great impact on global public health.
- Published
- 2020
3. Computer vision profiling of neurite outgrowth dynamics reveals spatio-temporal modularity of Rho GTPase signaling
- Author
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Fusco, Ludovico, Lefort, Riwal, Smith, Kevin, Benmansour, Fethallah, Gonzalez, German, Barillari, C, Rinn, Bernd, Fleuret, Francois, Fua, Pascal, Pertz, Olivier, Fusco, Ludovico, Lefort, Riwal, Smith, Kevin, Benmansour, Fethallah, Gonzalez, German, Barillari, C, Rinn, Bernd, Fleuret, Francois, Fua, Pascal, and Pertz, Olivier
- Abstract
Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neuriteinitiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present Neurite-Tracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth., QC 20160224. QC 20160319
- Published
- 2016
- Full Text
- View/download PDF
4. PKA-S6K1 Chimera with compound 1 (NU1085) bound
- Author
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Couty, S., primary, Westwood, I.M., additional, Kalusa, A., additional, Cano, C., additional, Travers, J., additional, Boxall, K., additional, Chow, C.L., additional, Burns, S., additional, Schmitt, J., additional, Pickard, L., additional, Barillari, C., additional, McAndrew, P.C., additional, Clarke, P.A., additional, Linardopoulos, S., additional, Griffin, R.J., additional, Aherne, G.W., additional, Raynaud, F.I., additional, Workman, P., additional, Jones, K., additional, and van Montfort, R.L.M., additional
- Published
- 2013
- Full Text
- View/download PDF
5. PKA-S6K1 Chimera with compound 15e (CCT147581) bound
- Author
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Couty, S., primary, Westwood, I.M., additional, Kalusa, A., additional, Cano, C., additional, Travers, J., additional, Boxall, K., additional, Chow, C.L., additional, Burns, S., additional, Schmitt, J., additional, Pickard, L., additional, Barillari, C., additional, McAndrew, P.C., additional, Clarke, P.A., additional, Linardopoulos, S., additional, Griffin, R.J., additional, Aherne, G.W., additional, Raynaud, F.I., additional, Workman, P., additional, Jones, K., additional, and van Montfort, R.L.M., additional
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- 2013
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6. PKA-S6K1 Chimera with Staurosporine bound
- Author
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Couty, S., primary, Westwood, I.M., additional, Kalusa, A., additional, Cano, C., additional, Travers, J., additional, Boxall, K., additional, Chow, C.L., additional, Burns, S., additional, Schmitt, J., additional, Pickard, L., additional, Barillari, C., additional, McAndrew, P.C., additional, Clarke, P.A., additional, Linardopoulos, S., additional, Griffin, R.J., additional, Aherne, G.W., additional, Raynaud, F.I., additional, Workman, P., additional, Jones, K., additional, and van Montfort, R.L.M., additional
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- 2013
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- View/download PDF
7. PKA-S6K1 Chimera with compound 21e (CCT239066) bound
- Author
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Couty, S., primary, Westwood, I.M., additional, Kalusa, A., additional, Cano, C., additional, Travers, J., additional, Boxall, K., additional, Chow, C.L., additional, Burns, S., additional, Schmitt, J., additional, Pickard, L., additional, Barillari, C., additional, McAndrew, P.C., additional, Clarke, P.A., additional, Linardopoulos, S., additional, Griffin, R.J., additional, Aherne, G.W., additional, Raynaud, F.I., additional, Workman, P., additional, Jones, K., additional, and van Montfort, R.L.M., additional
- Published
- 2013
- Full Text
- View/download PDF
8. PKA-S6K1 Chimera Apo
- Author
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Couty, S., primary, Westwood, I.M., additional, Kalusa, A., additional, Cano, C., additional, Travers, J., additional, Boxall, K., additional, Chow, C.L., additional, Burns, S., additional, Schmitt, J., additional, Pickard, L., additional, Barillari, C., additional, McAndrew, P.C., additional, Clarke, P.A., additional, Linardopoulos, S., additional, Griffin, R.J., additional, Aherne, G.W., additional, Raynaud, F.I., additional, Workman, P., additional, Jones, K., additional, and van Montfort, R.L.M., additional
- Published
- 2013
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9. Making the Difference in Occupational Health: Three Original and Significant Cases Presented at ICOH Congresses in the 20th Century
- Author
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Valeria Boccuni, Michele Augusto Riva, Seong-Kyu Kang, Caterina Barillari, Grazia Fortuna, Sergio Iavicoli, Antonio Valenti, Luigi Tomassini, Francesco Carnevale, Iavicoli, S, Valenti, A, Barillari, C, Fortuna, G, Boccuni, V, Carnevale, F, Riva, M, Kang, S, and Tomassini, L
- Subjects
medicine.medical_specialty ,History ,Occupational Safety ,Battle ,Vinyl chloride monomer ,media_common.quotation_subject ,history of medicine ,Transferability ,Psychological intervention ,ICOH ,Commission ,Occupational safety and health ,Ancylostomiasis ,ICOH repository, occupational health, history of medicine ,Carbon disulphide poisoning ,Occupational medicine ,Political science ,medicine ,Safety, Risk, Reliability and Quality ,Occupational Health ,media_common ,ICOH repository ,Chemical Health and Safety ,business.industry ,lcsh:Public aspects of medicine ,Public health ,Public Health, Environmental and Occupational Health ,MED/44 - MEDICINA DEL LAVORO ,lcsh:RA1-1270 ,Public relations ,ICOH heritage repository ,MED/02 - STORIA DELLA MEDICINA ,Original Article ,business ,Safety Research - Abstract
Background The aim of this study is to illustrate the historical role of the International Commission on Occupational Health (ICOH) congresses as an arena where national and international occupational medicine can dialogue and as the first example of scientific transferability of the research and prevention results that have had such an impact on global public health. Methods We used the ICOH Heritage Repository, in which ICOH congress proceedings (from the first congress in Milan in 1906 to the last congress, held in Dublin in 2018), are organised in an orderly way, updated and easily accessible according to open access logic. Results We describe studies by three physicians who submitted significant scientific work to ICOH congresses, one on the battle against ancylostomiasis (Volante, 1906), the second (Quarelli, 1928) on carbon disulphide poisoning, and the third (Viola, 1969) on the carcinogenicity of vinyl chloride monomer. Priority is given to Italian cases, on account of the authors’ obvious familiarity with the issues. Conclusion The visibility offered in ICOH conferences and their published proceedings has boosted the international spread of their findings, contributing to the scientific transferability of the research results and influencing the development of policies and prevention interventions that have had a great impact on global public health.
- Published
- 2020
10. Global Policy Responses to the COVID-19 Pandemic: Results of the ICOH Survey.
- Author
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Rondinone BM, Valenti A, Boccuni V, Cannone E, Boccuni F, Gagliardi D, Dionisi P, Barillari C, and Iavicoli S
- Abstract
Background: On the basis of its role for the development of occupational health research, information, good practices, the International Commission on Occupational Health (ICOH) launched the present survey to collect information on public health and prevention policies put in place by the governments of the countries in the world to contain the pandemic., Methods: A cross-sectional study was conducted through an online questionnaire focused on COVID-19 data, public health policies, prevention measures, support measures for economy, work, and education, personal protective equipment, intensive care units, contact tracing, return to work, and the role of ICOH against COVID-19. The questionnaire was administered to 113 ICOH National Secretaries and senior OSH experts. Collected data refer to the period ranging from the beginning of the pandemic in each country to June 30, 2020., Results: A total of 73 questionnaires from 73 countries around the world were considered valid, with a 64.6% response rate. Most of the respondents (71.2%) reported that the state of emergency was declared in their country, and 86.1% reported lockdown measures. Most of the respondents (66.7%) affirmed that the use of face masks was compulsory in their country. As for containment measures, 97.2% indicated that mass gatherings (meetings) were limited. Regarding workplace closing, the most affected sector was entertainment (90.1%)., Conclusion: The results of this survey are useful to gain a global view on COVID-19 policy responses at country level., Competing Interests: There are no conflicts of interest to declare., (© 2022 Occupational Safety and Health Research Institute.)
- Published
- 2022
- Full Text
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11. The future of scientific conferences in the era of the COVID-19 pandemic: Critical analysis and future perspectives.
- Author
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Valenti A, Fortuna G, Barillari C, Cannone E, Boccuni V, and Iavicoli S
- Subjects
- Humans, Information Dissemination, Pandemics, SARS-CoV-2, Travel, COVID-19 epidemiology, Congresses as Topic organization & administration, Telecommunications organization & administration
- Abstract
The global spread of COVID-19 pandemic forced the scientific community to identify new ways of exchanging and transferring the scientific knowledge, also considering that the measures taken to combat the pandemic, such as travel restrictions, closed borders and gathering bans, led to cancellations of many conferences, meetings and workshops. The enhancement of the existing digital platforms and the development of new systems to share scientific knowledge has allowed the scientific community to "meet" again in new virtual environments (e.g., Zoom, Cisco WebEx, Live Stream, Demio, GoToWebinar Seminar, Google Hangouts, Skype, Microsoft Teams, etc.), providing an unprecedented opportunity to reform methods of organizing academic conferences in all disciplines.Starting from the review of the existing literature, this study aimed at investigating the impact of the spreading of virtual conferences on the field of research. The SWOT analysis was used to identify strengths and weaknesses of the scientific conferences organized in the new format, as well as opportunities and threats created by the socio-economic and political context in the era of the COVID-19 pandemic.
- Published
- 2021
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- View/download PDF
12. Making the Difference in Occupational Health: Three Original and Significant Cases Presented at ICOH Congresses in the 20 th Century.
- Author
-
Iavicoli S, Valenti A, Barillari C, Fortuna G, Boccuni V, Carnevale F, Riva MA, Kang SK, and Tomassini L
- Abstract
Background: The aim of this study is to illustrate the historical role of the International Commission on Occupational Health (ICOH) congresses as an arena where national and international occupational medicine can dialogue and as the first example of scientific transferability of the research and prevention results that have had such an impact on global public health., Methods: We used the ICOH Heritage Repository, in which ICOH congress proceedings (from the first congress in Milan in 1906 to the last congress, held in Dublin in 2018), are organised in an orderly way, updated and easily accessible according to open access logic., Results: We describe studies by three physicians who submitted significant scientific work to ICOH congresses, one on the battle against ancylostomiasis (Volante, 1906), the second (Quarelli, 1928) on carbon disulphide poisoning, and the third (Viola, 1969) on the carcinogenicity of vinyl chloride monomer. Priority is given to Italian cases, on account of the authors' obvious familiarity with the issues., Conclusion: The visibility offered in ICOH conferences and their published proceedings has boosted the international spread of their findings, contributing to the scientific transferability of the research results and influencing the development of policies and prevention interventions that have had a great impact on global public health., Competing Interests: There are no conflicts of interest to declare., (© 2020 The Authors.)
- Published
- 2020
- Full Text
- View/download PDF
13. openBIS ELN-LIMS: an open-source database for academic laboratories.
- Author
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Barillari C, Ottoz DS, Fuentes-Serna JM, Ramakrishnan C, Rinn B, and Rudolf F
- Subjects
- Computer Systems, Information Systems, Software, User-Computer Interface, Biological Science Disciplines, Databases, Factual, Information Management, Laboratories
- Abstract
Unlabelled: The open-source platform openBIS (open Biology Information System) offers an Electronic Laboratory Notebook and a Laboratory Information Management System (ELN-LIMS) solution suitable for the academic life science laboratories. openBIS ELN-LIMS allows researchers to efficiently document their work, to describe materials and methods and to collect raw and analyzed data. The system comes with a user-friendly web interface where data can be added, edited, browsed and searched., Availability and Implementation: The openBIS software, a user guide and a demo instance are available at https://openbis-eln-lims.ethz.ch. The demo instance contains some data from our laboratory as an example to demonstrate the possibilities of the ELN-LIMS (Ottoz et al., 2014). For rapid local testing, a VirtualBox image of the ELN-LIMS is also available., (© The Author 2015. Published by Oxford University Press.)
- Published
- 2016
- Full Text
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14. Computer vision profiling of neurite outgrowth dynamics reveals spatiotemporal modularity of Rho GTPase signaling.
- Author
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Fusco L, Lefort R, Smith K, Benmansour F, Gonzalez G, Barillari C, Rinn B, Fleuret F, Fua P, and Pertz O
- Subjects
- Animals, Mice, Neurites metabolism, Phenotype, Tumor Cells, Cultured, Neurites enzymology, Signal Transduction, Spatio-Temporal Analysis, rhoA GTP-Binding Protein metabolism
- Abstract
Rho guanosine triphosphatases (GTPases) control the cytoskeletal dynamics that power neurite outgrowth. This process consists of dynamic neurite initiation, elongation, retraction, and branching cycles that are likely to be regulated by specific spatiotemporal signaling networks, which cannot be resolved with static, steady-state assays. We present NeuriteTracker, a computer-vision approach to automatically segment and track neuronal morphodynamics in time-lapse datasets. Feature extraction then quantifies dynamic neurite outgrowth phenotypes. We identify a set of stereotypic neurite outgrowth morphodynamic behaviors in a cultured neuronal cell system. Systematic RNA interference perturbation of a Rho GTPase interactome consisting of 219 proteins reveals a limited set of morphodynamic phenotypes. As proof of concept, we show that loss of function of two distinct RhoA-specific GTPase-activating proteins (GAPs) leads to opposite neurite outgrowth phenotypes. Imaging of RhoA activation dynamics indicates that both GAPs regulate different spatiotemporal Rho GTPase pools, with distinct functions. Our results provide a starting point to dissect spatiotemporal Rho GTPase signaling networks that regulate neurite outgrowth., (© 2016 Fusco et al.)
- Published
- 2016
- Full Text
- View/download PDF
15. The discovery of potent ribosomal S6 kinase inhibitors by high-throughput screening and structure-guided drug design.
- Author
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Couty S, Westwood IM, Kalusa A, Cano C, Travers J, Boxall K, Chow CL, Burns S, Schmitt J, Pickard L, Barillari C, McAndrew PC, Clarke PA, Linardopoulos S, Griffin RJ, Aherne GW, Raynaud FI, Workman P, Jones K, and van Montfort RL
- Subjects
- Cell Line, Tumor, Cyclic AMP-Dependent Protein Kinases antagonists & inhibitors, Cyclic AMP-Dependent Protein Kinases metabolism, Drug Design, High-Throughput Screening Assays methods, Humans, Imidazoles chemistry, Imidazoles pharmacology, Models, Molecular, Phosphorylation, Protein Kinase Inhibitors chemistry, Recombinant Fusion Proteins chemistry, Ribosomal Protein S6 Kinases, 90-kDa metabolism, Signal Transduction, Structure-Activity Relationship, Urinary Bladder Neoplasms drug therapy, Urinary Bladder Neoplasms enzymology, Protein Kinase Inhibitors pharmacology, Ribosomal Protein S6 Kinases, 90-kDa antagonists & inhibitors
- Abstract
The ribosomal P70 S6 kinases play a crucial role in PI3K/mTOR regulated signalling pathways and are therefore potential targets for the treatment of a variety of diseases including diabetes and cancer. In this study we describe the identification of three series of chemically distinct S6K1 inhibitors. In addition, we report a novel PKA-S6K1 chimeric protein with five mutations in or near its ATP-binding site, which was used to determine the binding mode of two of the three inhibitor series, and provided a robust system to aid the optimisation of the oxadiazole-substituted benzimidazole inhibitor series. We show that the resulting oxadiazole-substituted aza-benzimidazole is a potent and ligand efficient S6 kinase inhibitor, which blocks the phosphorylation of RPS6 at Ser235/236 in TSC negative HCV29 human bladder cancer cells by inhibiting S6 kinase activity and thus provides a useful tool compound to investigate the function of S6 kinases.
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- 2013
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16. Analysis of water patterns in protein kinase binding sites.
- Author
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Barillari C, Duncan AL, Westwood IM, Blagg J, and van Montfort RL
- Subjects
- Adenosine Triphosphate chemistry, Adenosine Triphosphate metabolism, Binding Sites, Cluster Analysis, Databases, Protein, Humans, Models, Molecular, Protein Conformation, Protein Kinases metabolism, Water metabolism, Protein Kinases chemistry, Water chemistry
- Abstract
Deregulation of protein kinases is associated with numerous diseases, making them important targets for drug discovery. The majority of drugs target the catalytic site of these proteins, but due to the high level of similarity within the ATP binding sites of protein kinases, it is often difficult to achieve the required pharmacological selectivity. In this study, we describe the identification and subsequent analysis of water patterns in the ATP binding sites of 171 protein kinase structures, comprising 19 different kinases from various branches of the kinome, and demonstrate that structurally similar binding sites often have significantly different water patterns. We show that the observed variations in water patterns of different, but structurally similar kinases can be exploited in the structure-based design of potent and selective kinase inhibitors., (Copyright © 2011 Wiley-Liss, Inc.)
- Published
- 2011
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17. Benzimidazole inhibitors induce a DFG-out conformation of never in mitosis gene A-related kinase 2 (Nek2) without binding to the back pocket and reveal a nonlinear structure-activity relationship.
- Author
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Solanki S, Innocenti P, Mas-Droux C, Boxall K, Barillari C, van Montfort RL, Aherne GW, Bayliss R, and Hoelder S
- Subjects
- Animals, Benzamides chemistry, Benzamides pharmacology, Benzimidazoles chemistry, Benzimidazoles pharmacology, Binding Sites, Crystallography, X-Ray, Female, Humans, In Vitro Techniques, Male, Mice, Microsomes, Liver drug effects, Microsomes, Liver enzymology, NIMA-Related Kinases, Phosphorylation, Protein Binding, Protein Conformation, Protein Serine-Threonine Kinases chemistry, Stereoisomerism, Structure-Activity Relationship, Benzamides chemical synthesis, Benzimidazoles chemical synthesis, Models, Molecular, Protein Serine-Threonine Kinases antagonists & inhibitors
- Abstract
We describe herein the structure-activity relationship (SAR) and cocrystal structures of a series of Nek2 inhibitors derived from the published polo-like kinase 1 (Plk1) inhibitor (R)-1. Our studies reveal a nonlinear SAR for Nek2 and our cocrystal structures show that compounds in this series bind to a DFG-out conformation of Nek2 without extending into the enlarged back pocket commonly found in this conformation. These observations were further investigated, and structure-based design led to Nek2 inhibitors derived from (R)-1 with more than a hundred-fold selectivity against Plk1.
- Published
- 2011
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18. Aminopyrazine inhibitors binding to an unusual inactive conformation of the mitotic kinase Nek2: SAR and structural characterization.
- Author
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Whelligan DK, Solanki S, Taylor D, Thomson DW, Cheung KM, Boxall K, Mas-Droux C, Barillari C, Burns S, Grummitt CG, Collins I, van Montfort RL, Aherne GW, Bayliss R, and Hoelder S
- Subjects
- Crystallography, X-Ray, Humans, NIMA-Related Kinases, Phosphorylation, Protein Binding, Protein Conformation, Protein Serine-Threonine Kinases chemistry, Pyrazines chemistry, Stereoisomerism, Structure-Activity Relationship, Models, Molecular, Protein Serine-Threonine Kinases antagonists & inhibitors, Pyrazines chemical synthesis
- Abstract
We report herein the first systematic exploration of inhibitors of the mitotic kinase Nek2. Starting from HTS hit aminopyrazine 2, compounds with improved activity were identified using structure-based design. Our structural biology investigations reveal two notable observations. First, 2 and related compounds bind to an unusual, inactive conformation of the kinase which to the best of our knowledge has not been reported for other types of kinase inhibitors. Second, a phenylalanine residue at the center of the ATP pocket strongly affects the ability of the inhibitor to bind to the protein. The implications of these observations are discussed, and the work described here defines key features for potent and selective Nek2 inhibition, which will aid the identification of more advanced inhibitors of Nek2.
- Published
- 2010
- Full Text
- View/download PDF
19. Targeting HSP70: the second potentially druggable heat shock protein and molecular chaperone?
- Author
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Powers MV, Jones K, Barillari C, Westwood I, van Montfort RL, and Workman P
- Subjects
- Animals, Binding Sites, DNA-Binding Proteins metabolism, HSP70 Heat-Shock Proteins metabolism, HSP90 Heat-Shock Proteins antagonists & inhibitors, HSP90 Heat-Shock Proteins metabolism, Heat Shock Transcription Factors, Mice, Protein Folding, Protein Structure, Tertiary, Small Molecule Libraries chemistry, Small Molecule Libraries pharmacology, Transcription Factors metabolism, HSP70 Heat-Shock Proteins antagonists & inhibitors, Molecular Chaperones metabolism
- Abstract
The HSF1-mediated stress response pathway is steadily gaining momentum as a critical source of targets for cancer therapy. Key mediators of this pathway include molecular chaperones such as heat shock protein (HSP) 90. There has been considerable progress in targeting HSP90 and the preclinical efficacy and signs of early clinical activity of HSP90 inhibitors have provided proof-of-concept for targeting this group of proteins. The HSP70 family of molecular chaperones are also key mediators of the HSF-1-stress response pathway and have multiple additional roles in protein folding, trafficking and degradation, as well as regulating apoptosis. Genetic and biochemical studies have supported the discovery of HSP70 inhibitors which have the potential for use as single agents or in combination to enhance the effects of classical chemotherapeutic or molecularly targeted agents including HSP90 inhibitors. Here we provide a perspective on the progress made so far in designing agents which target the HSP70 family.
- Published
- 2010
- Full Text
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20. Hot-spots-guided receptor-based pharmacophores (HS-Pharm): a knowledge-based approach to identify ligand-anchoring atoms in protein cavities and prioritize structure-based pharmacophores.
- Author
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Barillari C, Marcou G, and Rognan D
- Subjects
- Ligands, Models, Molecular, Protein Conformation, Proteins chemistry
- Abstract
The design of biologically active compounds from ligand-free protein structures using a structure-based approach is still a major challenge. In this paper, we present a fast knowledge-based approach (HS-Pharm) that allows the prioritization of cavity atoms that should be targeted for ligand binding, by training machine learning algorithms with atom-based fingerprints of known ligand-binding pockets. The knowledge of hot spots for ligand binding is here used for focusing structure-based pharmacophore models. Three targets of pharmacological interest (neuraminidase, beta2 adrenergic receptor, and cyclooxygenase-2) were used to test the evaluated methodology, and the derived structure-based pharmacophores were used in retrospective virtual screening studies. The current study shows that structure-based pharmacophore screening is a powerful technique for the fast identification of potential hits in a chemical library, and that it is a valid alternative to virtual screening by molecular docking.
- Published
- 2008
- Full Text
- View/download PDF
21. Domain versatility in plant AB-toxins: evidence for a local, pH-dependent rearrangement in the 2gamma lectin site of the mistletoe lectin by applying ligand derivatives and modelling.
- Author
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Jiménez M, André S, Barillari C, Romero A, Rognan D, Gabius HJ, and Solís D
- Subjects
- Asialoglycoproteins chemistry, Crystallography, Fetuins, Galactose chemistry, Hydrogen-Ion Concentration, Ligands, Methylgalactosides chemistry, Models, Chemical, Plant Lectins toxicity, Protein Structure, Tertiary, Ricin chemistry, Toxins, Biological toxicity, Tyrosine chemistry, alpha-Fetoproteins chemistry, Plant Lectins chemistry, Toxins, Biological chemistry, Viscum album toxicity
- Abstract
Mistletoe lectin is a potent biohazard. Lectin activity in the toxic dimer primarily originates from the 2gamma-subdomain (Tyr-site) of the B-subunit. Crystallographic information on lectin-sugar complexes is available only at acidic pH, where lectin activity is low. Thus, we mapped ligand-binding properties including comparison to ricin's Tyr-site at neutral pH. Using these results and molecular dynamics simulations, a local conformational change was rendered likely. The obtained structural information is valuable for the design of potent inhibitors.
- Published
- 2008
- Full Text
- View/download PDF
22. Classification of water molecules in protein binding sites.
- Author
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Barillari C, Taylor J, Viner R, and Essex JW
- Subjects
- HIV Protease chemistry, Hydrogen Bonding, Ligands, Models, Molecular, Protein Binding, Solvents chemistry, Statistics as Topic, Thermodynamics, Algorithms, Computer Simulation, Proteins chemistry, Water chemistry
- Abstract
Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.
- Published
- 2007
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23. [The clofibrate-dipyridamole combination in the treatment of athero-arteriosclerotic vasculopathy].
- Author
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Parenti M, Pasquali R, Bianchi V, Barillari C, and Vezzadini P
- Subjects
- Adult, Aged, Drug Combinations, Drug Evaluation, Female, Fibrinogen analysis, Glucose Tolerance Test, Humans, Lipids blood, Male, Middle Aged, Platelet Aggregation drug effects, Prothrombin analysis, Arteriosclerosis drug therapy, Clofibrate therapeutic use, Coronary Disease drug therapy, Dipyridamole therapeutic use
- Abstract
A group of patients with athero-arteriosclerotic vascular disease (coronary heart disease and atherosclerosis of the extremities) have been subjected to platelet antiaggregating-antidyslipidaemic treatment with a chlofibrate-dipyridamol association; a control series was treated with chlofibrate alone. Frequency of angina pectoris, pain intensity and trinitrine consumption ware evaluated in patients with coronary heart disease, claudicometry, oscillometry and thermometry in patients with atherosclerosis of the extremities. The following laboratory parameters were also analysed: cholesterolaemia, triglyceridaemia, prothrombin activity, fibrinogenaemia, uricaemia and tolerance of oral glucose loading. Analysis of the results has shown that the association improved the parameters considered in statistically significant fashion; chlofibrate alone led to significant modifications of coronaropathic group parameters (with the exception of pain intensity) whereas it did not lead to significant changes in parameters evaluated for atherosclerosis of the extremities. All laboratory parameters were modified favourably by the association to a statistically greater extent than by chlofibrate alone. Both the association and chlofibrate were well tolerated.
- Published
- 1979
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