33 results on '"Betzi, Stéphane"'
Search Results
2. ChemoDOTS: a web server to design chemistry-driven focused libraries.
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Hoffer, Laurent, Charifi-Hoareau, Guillaume, Barelier, Sarah, Betzi, Stéphane, Miller, Thomas, Morelli, Xavier, and Roche, Philippe
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- 2024
- Full Text
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3. From a drug repositioning to a structure-based drug design approach to tackle acute lymphoblastic leukemia.
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Saez-Ayala, Magali, Hoffer, Laurent, Abel, Sébastien, Ben Yaala, Khaoula, Sicard, Benoit, Andrieu, Guillaume P., Latiri, Mehdi, Davison, Emma K., Ciufolini, Marco A., Brémond, Paul, Rebuffet, Etienne, Roche, Philippe, Derviaux, Carine, Voisset, Edwige, Montersino, Camille, Castellano, Remy, Collette, Yves, Asnafi, Vahid, Betzi, Stéphane, and Dubreuil, Patrice
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DRUG repositioning ,DRUG design ,LYMPHOBLASTIC leukemia ,ACUTE leukemia ,DEOXYRIBONUCLEOTIDES - Abstract
Cancer cells utilize the main de novo pathway and the alternative salvage pathway for deoxyribonucleotide biosynthesis to achieve adequate nucleotide pools. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for anti-proliferative therapies for cancers where it is essential. Here, we present the development of a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. This strategy allows an acceleration of the hit-to-lead process by gradually implementing key chemical modifications to increase affinity and activity. Our lead compound, OR0642, is more than 1000 times more potent than its initial parent compound, masitinib, previously identified from a drug repositioning approach. OR0642 in combination with a physiological inhibitor of the de novo pathway doubled the survival rate in a human T-cell acute lymphoblastic leukemia patient-derived xenograft mouse model, demonstrating the proof-of-concept of this drug design strategy. Deoxycytidine kinase is the rate-limiting enzyme of the salvage pathway and it has recently emerged as a target for antiproliferative therapies for cancers where it is essential. Here, the authors develop a potent inhibitor applying an iterative multidisciplinary approach, which relies on computational design coupled with experimental evaluations. [ABSTRACT FROM AUTHOR]
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- 2023
- Full Text
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4. Functional Consequence of Covalent Reaction of Phosphoenolpyruvate with UDP-N-acetylglucosamine 1-Carboxyvinyltransferase (MurA)
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Zhu, Jin-Yi, Yang, Yan, Han, Huijong, Betzi, Stephane, Olesen, Sanne H., Marsilio, Frank, and Schönbrunn, Ernst
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- 2012
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5. Protein-Protein Interaction Inhibition (2P2I) Combining High Throughput and Virtual Screening: Application to the HIV-1 Nef Protein
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Betzi, Stéphane, Restouin, Audrey, Opi, Sandrine, Arold, Stefan T., Parrot, Isabelle, Guerlesquin, Françoise, Morelli, Xavier, and Collette, Yves
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- 2007
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6. An integrative in silico methodology for the identification of modulators of macrophage migration inhibitory factor (MIF) tautomerase activity
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El Turk, Farah, Fauvet, Bruno, Ouertatani-Sakouhi, Hajer, Lugari, Adrien, Betzi, Stephane, Roche, Philippe, Morelli, Xavier, and Lashuel, Hilal A.
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- 2010
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7. Identification of allosteric inhibitors blocking the hepatitis C virus polymerase NS5B in the RNA synthesis initiation step
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Betzi, Stéphane, Eydoux, Cécilia, Bussetta, Cécile, Blemont, Marilyne, Leyssen, Pieter, Debarnot, Claire, Ben-Rahou, Mohamed, Haiech, Jacques, Hibert, Marcel, Gueritte, Françoise, Grierson, David S., Romette, Jean-Louis, Guillemot, Jean-Claude, Neyts, Johan, Alvarez, Karine, Morelli, Xavier, Dutartre, Hélène, and Canard, Bruno
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- 2009
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8. Focused chemical libraries – design and enrichment: an example of protein–protein interaction chemical space
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Zhang, Xu, Betzi, Stéphane, Morelli, Xavier, and Roche, Philippe
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- 2014
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9. CRCM5484: A BET-BDII Selective Compound with Differential Anti-leukemic Drug Modulation.
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Carrasco, Kendall, Montersino, Camille, Derviaux, Carine, Saez-Ayala, Magali, Hoffer, Laurent, Restouin, Audrey, Castellano, Rémy, Casassa, Justine, Roche, Philippe, Pasquier, Eddy, Combes, Sébastien, Morelli, Xavier, Collette, Yves, and Betzi, Stéphane
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- 2022
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10. 2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions
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Basse, Marie Jeanne, Betzi, Stéphane, Bourgeas, Raphaël, Bouzidi, Sofia, Chetrit, Bernard, Hamon, Véronique, Morelli, Xavier, and Roche, Philippe
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- 2013
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11. Revisiting the Molecular Interactions between the Tumor Protein TCTP and the Drugs Sertraline/Thioridazine.
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Malard, Florian, Jacquet, Eric, Nhiri, Naima, Sizun, Christina, Chabrier, Amélie, Messaoudi, Samir, Dejeu, Jérôme, Betzi, Stéphane, Zhang, Xu, Thureau, Aurélien, and Lescop, Ewen
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- 2022
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12. In silico molecular target prediction unveils mebendazole as a potent MAPK14 inhibitor.
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Ariey‐Bonnet, Jeremy, Carrasco, Kendall, Le Grand, Marion, Hoffer, Laurent, Betzi, Stéphane, Feracci, Mikael, Tsvetkov, Philipp, Devred, Francois, Collette, Yves, Morelli, Xavier, Ballester, Pedro, and Pasquier, Eddy
- Abstract
The concept of polypharmacology involves the interaction of drug molecules with multiple molecular targets. It provides a unique opportunity for the repurposing of already‐approved drugs to target key factors involved in human diseases. Herein, we used an in silico target prediction algorithm to investigate the mechanism of action of mebendazole, an antihelminthic drug, currently repurposed in the treatment of brain tumors. First, we confirmed that mebendazole decreased the viability of glioblastoma cells in vitro (IC50 values ranging from 288 nm to 2.1 µm). Our in silico approach unveiled 21 putative molecular targets for mebendazole, including 12 proteins significantly upregulated at the gene level in glioblastoma as compared to normal brain tissue (fold change > 1.5; P < 0.0001). Validation experiments were performed on three major kinases involved in cancer biology: ABL1, MAPK1/ERK2, and MAPK14/p38α. Mebendazole could inhibit the activity of these kinases in vitro in a dose‐dependent manner, with a high potency against MAPK14 (IC50 = 104 ± 46 nm). Its direct binding to MAPK14 was further validated in vitro, and inhibition of MAPK14 kinase activity was confirmed in live glioblastoma cells. Consistent with biophysical data, molecular modeling suggested that mebendazole was able to bind to the catalytic site of MAPK14. Finally, gene silencing demonstrated that MAPK14 is involved in glioblastoma tumor spheroid growth and response to mebendazole treatment. This study thus highlighted the role of MAPK14 in the anticancer mechanism of action of mebendazole and provides further rationale for the pharmacological targeting of MAPK14 in brain tumors. It also opens new avenues for the development of novel MAPK14/p38α inhibitors to treat human diseases. [ABSTRACT FROM AUTHOR]
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- 2020
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13. Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis
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Cartier-Michaud, Amandine, Bailly, Anne-Laure, Betzi, Stéphane, Shi, Xiaoli, Lissitzky, Jean-Claude, Zarubica, Ana, Sergé, Arnauld, ROCHE, Philippe, Lugari, Adrien, HAMON, Véronique, Bardin, Florence, Derviaux, Carine, Lembo, Frédérique, Audebert, Stéphane, Marchetto, Sylvie, Durand, Bénédicte, Borg, Jean-Paul, Shi, Ning, Morelli, Xavier, Aurrand-Lions, Michel, Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre d'Immunologie de Marseille - Luminy (CIML), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), ANR-11-IDEX-0001,Amidex,INITIATIVE D'EXCELLENCE AIX MARSEILLE UNIVERSITE(2011), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)
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Male ,Physiology ,[SDV]Life Sciences [q-bio] ,Golgi Apparatus ,Mice ,Animal Cells ,Reproductive Physiology ,Spermatocytes ,Medicine and Health Sciences ,Cell Cycle and Cell Division ,Testes ,Cells, Cultured ,Staining ,Chromosome Biology ,Intracellular Signaling Peptides and Proteins ,Specimen preparation and treatment ,Spermatids ,humanities ,Protein Transport ,Meiosis ,Seminiferous tubules ,Cell Processes ,cardiovascular system ,Cellular Types ,Anatomy ,Cellular Structures and Organelles ,Genital Anatomy ,Protein Binding ,Research Article ,endocrine system ,lcsh:QH426-470 ,education ,Immunoglobulins ,[SDV.BC]Life Sciences [q-bio]/Cellular Biology ,Germ cells ,Acrosomes ,Animals ,Spermatogenesis ,Binding Sites ,fungi ,Reproductive System ,DAPI staining ,Membrane Proteins ,Biology and Life Sciences ,Cell Biology ,Spermatogonia ,Sperm ,Mice, Inbred C57BL ,Research and analysis methods ,lcsh:Genetics ,Nuclear staining ,Carrier Proteins ,Cell Adhesion Molecules - Abstract
Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes., Author summary Spermatogenesis defects are a common cause of male sterility. Spermatogenesis occurs in the seminiferous tubules of the testes and involves adhesive interactions between developing germ cells and Sertoli cells. Knock-out mouse models identified several adhesion molecules that are critically involved in spermatogenesis. We previously demonstrated that the Junctional Adhesion Molecule-C (JAM-C) plays a crucial role in establishing spermatids polarity. The latter involves rearrangements of the Golgi apparatus in spermatids which contribute to acrosome formation. The present study demonstrated that the C-terminal cytosolic region of JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55) encoded by Gorasp2 and that spermatogenesis was impaired in Gorasp2-deficient mice. We developed an inhibitor of GRASP55 interaction with JAM-C and demonstrated that treatment of wild-type mice with the inhibitory compound induced germ cell loss. Therefore, the male infertility-associated pathway identified in this study is important not only from a genetic point of view, but also as a potential target for male contraception.
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- 2017
14. Integrated Strategy for Lead Optimization Based on Fragment Growing: The Diversity-Oriented-Target-Focused-Synthesis Approach.
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Hoffer, Laurent, Voitovich, Yuliia V., Raux, Brigitt, Carrasco, Kendall, Muller, Christophe, Fedorov, Aleksey Y., Derviaux, Carine, Amouric, Agnès, Betzi, Stéphane, Horvath, Dragos, Varnek, Alexandre, Collette, Yves, Combes, Sébastien, Roche, Philippe, and Morelli, Xavier
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- 2018
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15. Structural recognition mechanisms between human Src homology domain 3 (SH3) and ALG-2-interacting protein X (Alix)
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Shi, Xiaoli, Betzi, Stephane, Lugari, Adrien, Opi, Sandrine, Restouin, Audrey, Parrot, Isabelle, Martinez, Jean, Zimmermann, Pascale, Lecine, Patrick, Huang, Mingdong, Arold, Stefan T., Collette, Yves, and Morelli, Xavier
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- 2012
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16. Mutational phospho-mimicry reveals a regulatory role for the XRCC4 and XLF C-terminal tails in modulating DNA bridging during classical non-homologous end joining.
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Normanno, Davide, Négrel, Aurélie, de Melo, Abinadabe J., Betzi, Stéphane, Meek, Katheryn, and Modesti, Mauro
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- 2017
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17. Exploring Selective Inhibition of the First Bromodomain of the Human Bromodomain and Extra-terminal Domain (BET) Proteins.
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Raux, Brigitt, Voitovich, Yuliia, Derviaux, Carine, Lugari, Adrien, Rebuffet, Etienne, Milhas, Sabine, Priet, Stéphane, Roux, Thomas, Trinquet, Eric, Guillemot, Jean-Claude, Knapp, Stefan, Brunel, Jean-Michel, Fedorov, Alexey Yu., Collette, Yves, Roche, Philippe, Betzi, Stéphane, Combes, Sébastien, and Morelli, Xavier
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- 2016
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18. 2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions.
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Basse, Marie-Jeanne, Betzi, Stéphane, Morelli, Xavier, and Roche, Philippe
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GENETIC databases , *PROTEIN-protein interactions , *SMALL molecules , *INTERNET servers , *PROTEIN-ligand interactions - Abstract
2P2Idb is a hand-curated structural database dedicated to protein-protein interactions with known small molecule orthosteric modulators. It compiles the structural information related to orthosteric inhibitors and their target [i.e. related 3D structures available in the RCSB Protein Data Bank (PDB)] and provides links to other useful databases. 2P2Idb includes all interactions for which both the protein-protein and protein-inhibitor complexes have been structurally characterized. Since its first release in 2010, the database has grown constantly and the current version contains 27 protein-protein complexes and 274 protein-inhibitor complexes corresponding to 242 unique small molecule inhibitors which represent almost a 5-fold increase compared to the previous version. A number of new data have been added, including new protein-protein complexes, binding affinities, molecular descriptors, precalculated interface parameters and links to other webservers. A new query tool has been implemented to search for inhibitors within the database using standard molecular descriptors. A novel version of the 2P2I-inspector tool has been implemented to calculate a series of physical and chemical parameters of the protein interfaces. Several geometrical parameters including planarity, eccentricity and circularity have been added as well as customizable distance cutoffs. This tool has also been extended to protein-ligand interfaces. The 2P2I database thus represents a wealth of structural source of information for scientists interested in the properties of protein-protein interactions and the design of protein-protein interaction modulators. [ABSTRACT FROM AUTHOR]
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- 2016
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19. Structural and Biochemical Characterization of the Cop9 Signalosome CSN5/CSN6 Heterodimer.
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Birol, Melissa, Enchev, Radoslav Ivanov, Padilla, André, Stengel, Florian, Aebersold, Ruedi, Betzi, Stéphane, Yang, Yinshan, Hoh, François, Peter, Matthias, Dumas, Christian, and Echalier, Aude
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UBIQUITIN ligases ,HETERODIMERS ,GENETIC regulation ,MASS spectrometry ,UBIQUITINATION ,PROTEASOMES ,PROTEIN-protein interactions - Abstract
The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core. [ABSTRACT FROM AUTHOR]
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- 2014
- Full Text
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20. Crystal Structure of the Vaccinia Virus DNA Polymerase Holoenzyme Subunit D4 in Complex with the A20 N-Terminal Domain.
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Contesto-Richefeu, Céline, Tarbouriech, Nicolas, Brazzolotto, Xavier, Betzi, Stéphane, Morelli, Xavier, Burmeister, Wim P., and Iseni, Frédéric
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VACCINIA ,DNA polymerases ,URACIL-DNA glycosylase ,HETERODIMERS ,DNA synthesis ,AMINO acids ,ANTIVIRAL agents - Abstract
Vaccinia virus polymerase holoenzyme is composed of the DNA polymerase E9, the uracil-DNA glycosylase D4 and A20, a protein with no known enzymatic activity. The D4/A20 heterodimer is the DNA polymerase co-factor whose function is essential for processive DNA synthesis. Genetic and biochemical data have established that residues located in the N-terminus of A20 are critical for binding to D4. However, no information regarding the residues of D4 involved in A20 binding is yet available. We expressed and purified the complex formed by D4 and the first 50 amino acids of A20 (D4/A20
1–50 ). We showed that whereas D4 forms homodimers in solution when expressed alone, D4/A201–50 clearly behaves as a heterodimer. The crystal structure of D4/A201–50 solved at 1.85 Å resolution reveals that the D4/A20 interface (including residues 167 to 180 and 191 to 206 of D4) partially overlaps the previously described D4/D4 dimer interface. A201–50 binding to D4 is mediated by an α-helical domain with important leucine residues located at the very N-terminal end of A20 and a second stretch of residues containing Trp43 involved in stacking interactions with Arg167 and Pro173 of D4. Point mutations of the latter residues disturb D4/A201–50 formation and reduce significantly thermal stability of the complex. Interestingly, small molecule docking with anti-poxvirus inhibitors selected to interfere with D4/A20 binding could reproduce several key features of the D4/A201–50 interaction. Finally, we propose a model of D4/A201–50 in complex with DNA and discuss a number of mutants described in the literature, which affect DNA synthesis. Overall, our data give new insights into the assembly of the poxvirus DNA polymerase cofactor and may be useful for the design and rational improvement of antivirals targeting the D4/A20 interface. [ABSTRACT FROM AUTHOR]- Published
- 2014
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- View/download PDF
21. Stereoselective synthesis of original spirolactams displaying promising folded structures.
- Author
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Chaubet, Guilhem, Coursindel, Thibault, Morelli, Xavier, Betzi, Stéphane, Roche, Philippe, Guari, Yannick, Lebrun, Aurélien, Toupet, Loïc, Collette, Yves, Parrot, Isabelle, and Martinez, Jean
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- 2013
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22. Prevalence, Specificity and Determinants of Lipid-Interacting PDZ Domains from an In-Cell Screen and In Vitro Binding Experiments.
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Ivarsson, Ylva, Wawrzyniak, Anna Maria, Kashyap, Rudra, Polanowska, Jolanta, Betzi, Stéphane, Lembo, Frédérique, Vermeiren, Elke, Chiheb, Driss, Lenfant, Nicolas, Morelli, Xavier, Borg, Jean-Paul, Reboul, Jérôme, and Zimmermann, Pascale
- Subjects
PDZ proteins ,PROTEIN-protein interactions ,PHOSPHOINOSITIDES ,GENETIC regulation ,CELLULAR signal transduction ,RECOMBINANT proteins ,PROTEOMICS - Abstract
Background: PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited. Methodology/Principal Findings: We screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands. Conclusions/Significance: Our screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands. [ABSTRACT FROM AUTHOR]
- Published
- 2013
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23. Comparative Virtual and Experimental Medium Throughput Screening for Hepatitis C Virus Polymerase Inhibitors
- Author
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Dutartre, Helene, Bussetta, Cecile, Betzi, Stephane, Boretto-Soler, Joelle, Debarnot, Claire, Ben-Rahou, Mohamed, Romette, Jean-Louis, Guillemot, Jean Claude, Alvarez, Karine, Morelli, Xavier, and Canard, Bruno
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- 2008
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24. Structural and Biochemical Characterization of the Cop9 Signalosome CSN5/CSN6 Heterodimer
- Author
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Birol, Melissa, Enchev, Radoslav Ivanov, Padilla, André, Stengel, Florian, Aebersold, Ruedi, Betzi, Stéphane, Yang, Yinshan, Hoh, François, Peter, Matthias, Dumas, Christian, and Echalier, Aude
- Subjects
3. Good health - Abstract
The Cop9 signalosome complex (CSN) regulates the functional cycle of the major E3 ubiquitin ligase family, the cullin RING E3 ubiquitin ligases (CRLs). Activated CRLs are covalently modified by the ubiquitin-like protein Nedd8 (neural precursor cell expressed developmentally down-regulated protein 8). CSN serves an essential role in myriad cellular processes by reversing this modification through the isopeptidase activity of its CSN5 subunit. CSN5 alone is inactive due to an auto-inhibited conformation of its catalytic domain. Here we report the molecular basis of CSN5 catalytic domain activation and unravel a molecular hierarchy in CSN deneddylation activity. The association of CSN5 and CSN6 MPN (for Mpr1/Pad1 N-terminal) domains activates its isopeptidase activity. The CSN5/CSN6 module, however, is inefficient in CRL deneddylation, indicating a requirement of further elements in this reaction such as other CSN subunits. A hybrid molecular model of CSN5/CSN6 provides a structural framework to explain these functional observations. Docking this model into a published CSN electron density map and using distance constraints obtained from cross-linking coupled to mass-spectrometry, we find that the C-termini of the CSN subunits could form a helical bundle in the centre of the structure. They likely play a key scaffolding role in the spatial organization of CSN and precise positioning of the dimeric MPN catalytic core., PLoS ONE, 9 (8), ISSN:1932-6203
25. CRCM5484: A BET- BDII Selective Compound With Differential Anti-Leukemic Drug Modulation
- Author
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Kendall Carrasco, Camille Montersino, Carine Derviaux, Magali Saez-Ayala, Laurent Hoffer, Audrey Restouin, Rémy Castellano, Justine Casassa, Philippe Roche, Eddy Pasquier, Sébastien Combes, Xavier Morelli, Yves Collette, Stéphane Betzi, Centre de Recherche en Cancérologie de Marseille (CRCM), Aix Marseille Université (AMU)-Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Fédération nationale des Centres de lutte contre le Cancer (FNCLCC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut Paoli-Calmettes, Fédération nationale des Centres de lutte contre le Cancer (FNCLCC), and Betzi, Stéphane
- Subjects
potentiation ,diversity-oriented library ,[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM] ,bone-marrow-derived stromal cell conditioned medium ,Nuclear Proteins ,Bromodomain ,Cell Cycle Proteins ,[SDV.CAN]Life Sciences [q-bio]/Cancer ,focused library ,drug discovery ,Small Molecule Libraries ,protein-protein interaction ,BDII selective inhibitor ,Structure-Activity Relationship ,modulation ,Protein Domains ,[SDV.CAN] Life Sciences [q-bio]/Cancer ,hit-to-lead ,[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Molecular Medicine ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,optimization ,Transcription Factors - Abstract
Differentially screening the Fr-PPIChem chemical library on the BET BRD4-BDII versus -BDI bromodomains led to the discovery of a BDII selective tetrahydropyridothienopyrimidinone (THPTP)-based compound. Structure-activity relationship (SAR) and hit-to-lead approaches allowed us to develop CRCM5484, a potent inhibitor of BET proteins with a preferential and 475-fold selectivity for the second bromodomain of the BRD3 protein (BRD3-BDII) over its first bromodomain (BRD3-BDI). Its very low activity was demonstrated in various cell-based assays, corresponding with recent data describing other selective BDII compounds. However, screening on a drug sensitivity and resistance-profiling platform revealed its ability to modulate the anti-leukemic activity in combination with various FDA-approved and/or in-development drugs in a cell- and context-dependent differential manner. Altogether, the results confirm the originality of the THPTP molecular mode of action in the BD cavity and its potential as starting scaffold for the development of potent and selective bromodomain inhibitors.
- Published
- 2022
26. Coronavirus Nsp10, a Critical Co-factor for Activation of Multiple Replicative Enzymes.
- Author
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Bouvet, Mickaël, Lugari, Adrien, Posthuma, Clara C., Zevenhoven, Jessika C., Bernard, Stéphanie, Betzi, Stéphane, Imbert, Isabelle, Canard, Bruno, Guillemot, Jean-Claude, Lécine, Patrick, Pfefferle, Susanne, Drosten, Christian, Snijder, Eric J., Decroly, Etienne, and Morelli, Xavier
- Subjects
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RNA synthesis , *SARS disease , *CORONAVIRUS diseases , *BIOLUMINESCENCE assay , *GENETIC mutation - Abstract
The RNA-synthesizing machinery of the severe acute respiratory syndrome Coronavirus (SARS-CoV) is composed of 16 non-structural proteins (nsp1-16) encoded by ORF1a/1b. The 148-amino acid nsp10 subunit contains two zinc fingers and is known to interact with both nsp14 and nsp16, stimulating their respective 3'-5' exoribonuclease and 2'-O-methyltransferase activities. Using alanine-scanning mutagenesis, in cellulo bioluminescence resonance energy transfer experiments, and in vitro pulldown assays, we have now identified the key residues on the nsp10 surface that interact with nsp14. The functional consequences of mutations introduced at these positions were first evaluated biochemically by monitoring nsp14 exoribonuclease activity. Disruption of the nsp10-nsp14 interaction abrogated the nsp10-driven activation of the nsp14 exoribonuclease. We further showed that the nsp10 surface interacting with nsp14 overlaps with the surface involved in the nsp10-mediated activation of nsp16 2'-O-methyltransferase activity, suggesting that nsp10 is a major regulator of SARS-CoV replicase function. In line with this notion, reverse genetics experiments supported an essential role of the nsp10 surface that interacts with nsp14 in SARS-CoV replication, as several mutations that abolished the interaction in vitro yielded a replication-negative viral phenotype. In contrast, mutants in which the nsp10-nsp16 interaction was disturbed proved to be crippled but viable. These experiments imply that the nsp10 surface that interacts with nsp14 and nsp16 and possibly other subunits of the viral replication complex may be a target for the development of antiviral compounds against pathogenic coronaviruses. [ABSTRACT FROM AUTHOR]
- Published
- 2014
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27. 4'-Ethynyl-2'-Deoxycytidine (EdC) Preferentially Targets Lymphoma and Leukemia Subtypes by Inducing Replicative Stress.
- Author
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Calbert ML, Chandramouly G, Adams CM, Saez-Ayala M, Kent T, Tyagi M, Ayyadevara VSSA, Wang Y, Krais JJ, Gordon J, Atkins J, Toma MM, Betzi S, Boghossian AS, Rees MG, Ronan MM, Roth JA, Goldman AR, Gorman N, Mitra R, Childers WE, Graña X, Skorski T, Johnson N, Hurtz C, Morelli X, Eischen CM, and Pomerantz RT
- Subjects
- Humans, Animals, Mice, Cell Line, Tumor, Lymphoma drug therapy, Lymphoma pathology, Lymphoma metabolism, Xenograft Model Antitumor Assays, Leukemia drug therapy, Leukemia pathology, Deoxycytidine Kinase metabolism, Deoxycytidine analogs & derivatives, Deoxycytidine pharmacology
- Abstract
Anticancer nucleosides are effective against solid tumors and hematologic malignancies, but typically are prone to nucleoside metabolism resistance mechanisms. Using a nucleoside-specific multiplexed high-throughput screening approach, we discovered 4'-ethynyl-2'-deoxycytidine (EdC) as a third-generation anticancer nucleoside prodrug with preferential activity against diffuse large B-cell lymphoma (DLBCL) and acute lymphoblastic leukemia (ALL). EdC requires deoxycytidine kinase (DCK) phosphorylation for its activity and induces replication fork arrest and accumulation of cells in S-phase, indicating it acts as a chain terminator. A 2.1Å cocrystal structure of DCK bound to EdC and UDP reveals how the rigid 4'-alkyne of EdC fits within the active site of DCK. Remarkably, EdC was resistant to cytidine deamination and SAMHD1 metabolism mechanisms and exhibited higher potency against ALL compared with FDA-approved nelarabine. Finally, EdC was highly effective against DLBCL tumors and B-ALL in vivo. These data characterize EdC as a preclinical nucleoside prodrug candidate for DLBCL and ALL., (©2023 American Association for Cancer Research.)
- Published
- 2024
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28. Discovery of a PDZ Domain Inhibitor Targeting the Syndecan/Syntenin Protein-Protein Interaction: A Semi-Automated "Hit Identification-to-Optimization" Approach.
- Author
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Hoffer L, Garcia M, Leblanc R, Feracci M, Betzi S, Ben Yaala K, Daulat AM, Zimmermann P, Roche P, Barral K, and Morelli X
- Subjects
- Drug Discovery, Syndecans metabolism, Syntenins, PDZ Domains
- Abstract
The rapid identification of early hits by fragment-based approaches and subsequent hit-to-lead optimization represents a challenge for drug discovery. To address this challenge, we created a strategy called "DOTS" that combines molecular dynamic simulations, computer-based library design (chemoDOTS) with encoded medicinal chemistry reactions, constrained docking, and automated compound evaluation. To validate its utility, we applied our DOTS strategy to the challenging target syntenin, a PDZ domain containing protein and oncology target. Herein, we describe the creation of a "best-in-class" sub-micromolar small molecule inhibitor for the second PDZ domain of syntenin validated in cancer cell assays. Key to the success of our DOTS approach was the integration of protein conformational sampling during hit identification stage and the synthetic feasibility ranking of the designed compounds throughout the optimization process. This approach can be broadly applied to other protein targets with known 3D structures to rapidly identify and optimize compounds as chemical probes and therapeutic candidates.
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- 2023
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29. Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis.
- Author
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Cartier-Michaud A, Bailly AL, Betzi S, Shi X, Lissitzky JC, Zarubica A, Sergé A, Roche P, Lugari A, Hamon V, Bardin F, Derviaux C, Lembo F, Audebert S, Marchetto S, Durand B, Borg JP, Shi N, Morelli X, and Aurrand-Lions M
- Subjects
- Animals, Binding Sites, Carrier Proteins chemistry, Carrier Proteins genetics, Cells, Cultured, Golgi Apparatus ultrastructure, Intracellular Signaling Peptides and Proteins, Male, Membrane Proteins chemistry, Membrane Proteins genetics, Mice, Mice, Inbred C57BL, Protein Binding, Protein Transport, Spermatogonia cytology, Carrier Proteins metabolism, Cell Adhesion Molecules metabolism, Golgi Apparatus metabolism, Immunoglobulins metabolism, Membrane Proteins metabolism, Spermatogenesis, Spermatogonia metabolism
- Abstract
Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes.
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- 2017
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30. Protein-Protein Interaction Inhibition (2P2I)-Oriented Chemical Library Accelerates Hit Discovery.
- Author
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Milhas S, Raux B, Betzi S, Derviaux C, Roche P, Restouin A, Basse MJ, Rebuffet E, Lugari A, Badol M, Kashyap R, Lissitzky JC, Eydoux C, Hamon V, Gourdel ME, Combes S, Zimmermann P, Aurrand-Lions M, Roux T, Rogers C, Müller S, Knapp S, Trinquet E, Collette Y, Guillemot JC, and Morelli X
- Subjects
- Crystallography, X-Ray, Protein Interaction Mapping, Drug Discovery, Proteins chemistry, Small Molecule Libraries
- Abstract
Protein-protein interactions (PPIs) represent an enormous source of opportunity for therapeutic intervention. We and others have recently pinpointed key rules that will help in identifying the next generation of innovative drugs to tackle this challenging class of targets within the next decade. We used these rules to design an oriented chemical library corresponding to a set of diverse "PPI-like" modulators with cores identified as privileged structures in therapeutics. In this work, we purchased the resulting 1664 structurally diverse compounds and evaluated them on a series of representative protein-protein interfaces with distinct "druggability" potential using homogeneous time-resolved fluorescence (HTRF) technology. For certain PPI classes, analysis of the hit rates revealed up to 100 enrichment factors compared with nonoriented chemical libraries. This observation correlates with the predicted "druggability" of the targets. A specific focus on selectivity profiles, the three-dimensional (3D) molecular modes of action resolved by X-ray crystallography, and the biological activities of identified hits targeting the well-defined "druggable" bromodomains of the bromo and extraterminal (BET) family are presented as a proof-of-concept. Overall, our present study illustrates the potency of machine learning-based oriented chemical libraries to accelerate the identification of hits targeting PPIs. A generalization of this method to a larger set of compounds will accelerate the discovery of original and potent probes for this challenging class of targets.
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- 2016
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31. Prevalence, specificity and determinants of lipid-interacting PDZ domains from an in-cell screen and in vitro binding experiments.
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Ivarsson Y, Wawrzyniak AM, Kashyap R, Polanowska J, Betzi S, Lembo F, Vermeiren E, Chiheb D, Lenfant N, Morelli X, Borg JP, Reboul J, and Zimmermann P
- Subjects
- Amino Acid Sequence, Bacterial Proteins, Binding Sites, Cell Line, Tumor, Genes, Reporter, High-Throughput Screening Assays, Humans, Immunoblotting, Kinetics, Ligands, Luminescent Proteins, Membrane Proteins chemistry, Models, Molecular, Molecular Sequence Data, Peptides chemistry, Phosphatidylinositols chemistry, Protein Binding, Recombinant Proteins chemistry, Recombinant Proteins metabolism, Surface Plasmon Resonance, Syntenins chemistry, Membrane Proteins metabolism, PDZ Domains, Peptides metabolism, Phosphatidylinositols metabolism, Syntenins metabolism
- Abstract
Background: PDZ domains are highly abundant protein-protein interaction modules involved in the wiring of protein networks. Emerging evidence indicates that some PDZ domains also interact with phosphoinositides (PtdInsPs), important regulators of cell polarization and signaling. Yet our knowledge on the prevalence, specificity, affinity, and molecular determinants of PDZ-PtdInsPs interactions and on their impact on PDZ-protein interactions is very limited., Methodology/principal Findings: We screened the human proteome for PtdInsPs interacting PDZ domains by a combination of in vivo cell-localization studies and in vitro dot blot and Surface Plasmon Resonance (SPR) experiments using synthetic lipids and recombinant proteins. We found that PtdInsPs interactions contribute to the cellular distribution of some PDZ domains, intriguingly also in nuclear organelles, and that a significant subgroup of PDZ domains interacts with PtdInsPs with affinities in the low-to-mid micromolar range. In vitro specificity for the head group is low, but with a trend of higher affinities for more phosphorylated PtdInsPs species. Other membrane lipids can assist PtdInsPs-interactions. PtdInsPs-interacting PDZ domains have generally high pI values and contain characteristic clusters of basic residues, hallmarks that may be used to predict additional PtdInsPs interacting PDZ domains. In tripartite binding experiments we established that peptide binding can either compete or cooperate with PtdInsPs binding depending on the combination of ligands., Conclusions/significance: Our screen substantially expands the set of PtdInsPs interacting PDZ domains, and shows that a full understanding of the biology of PDZ proteins will require a comprehensive insight into the intricate relationships between PDZ domains and their peptide and lipid ligands.
- Published
- 2013
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32. Protein-protein interaction inhibition (2P2I): fewer and fewer undruggable targets.
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Betzi S, Guerlesquin F, and Morelli X
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- Animals, Computational Biology trends, Computing Methodologies, Crystallography, X-Ray, Humans, Models, Molecular, Nuclear Magnetic Resonance, Biomolecular, Protein Binding, Proteins metabolism, Computational Biology methods, Drug Design, Proteins antagonists & inhibitors, Proteins chemistry
- Abstract
Low molecular weight inhibitors of Protein-Protein Interactions (PPI's) have been identified for a number of different systems indicating the viability of the computer-aided drug design approaches. However, pathways undertaken by researchers in pharmaceutical companies or in academic laboratories are not always clearly defined and the protocols that allow the identification of lead compounds often remain blurry. We will enumerate in this review the main approaches carried out to identify and validate PPI's inhibitors. Emphasis will be placed, in a first part, on issues of particular significance to PPI's such as the problem of identification and validation of interacting sites and on the methods that allow assessing the 3D structure of a targeted complex. On the second part of this review, we will define approaches that allow a rapid identification of hits capable of inhibiting PPI's. We will highlight the problem of the scoring functions and demonstrate that the majority of the functions available to researchers are not especially relevant for PPI's. We will define why consensus scoring can be an alternative and we will propose GFscore, a non linear ranked-by number consensus scoring function as a solution to this problem. We will finally discuss the actual challenges that still remain, particularly the problem of the treatment of the receptor flexibility and of the water molecules at the interface of the Protein-Protein complexes.
- Published
- 2009
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33. GFscore: a general nonlinear consensus scoring function for high-throughput docking.
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Betzi S, Suhre K, Chétrit B, Guerlesquin F, and Morelli X
- Subjects
- Quantitative Structure-Activity Relationship, Molecular Structure
- Abstract
Most of the recent published works in the field of docking and scoring protein/ligand complexes have focused on ranking true positives resulting from a Virtual Library Screening (VLS) through the use of a specified or consensus linear scoring function. In this work, we present a methodology to speed up the High Throughput Screening (HTS) process, by allowing focused screens or for hitlist triaging when a prohibitively large number of hits is identified in the primary screen, where we have extended the principle of consensus scoring in a nonlinear neural network manner. This led us to introduce a nonlinear Generalist scoring Function, GFscore, which was trained to discriminate true positives from false positives in a data set of diverse chemical compounds. This original Generalist scoring Function is a combination of the five scoring functions found in the CScore package from Tripos Inc. GFscore eliminates up to 75% of molecules, with a confidence rate of 90%. The final result is a Hit Enrichment in the list of molecules to investigate during a research campaign for biological active compounds where the remaining 25% of molecules would be sent to in vitro screening experiments. GFscore is therefore a powerful tool for the biologist, saving both time and money.
- Published
- 2006
- Full Text
- View/download PDF
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