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1. Identification of small molecules affecting the interaction between human hemoglobin and Staphylococcus aureus IsdB hemophore

Author

Cozzi, Monica, Failla, Mariacristina, Gianquinto, Eleonora, Kovachka, Sandra, Buoli Comani, Valeria, Compari, Carlotta, De Bei, Omar, Giaccari, Roberta, Marchesani, Francesco, Marchetti, Marialaura, Ronda, Luca, Rolando, Barbara, Baroni, Massimo, Cruciani, Gabriele, Campanini, Barbara, Bettati, Stefano, Faggiano, Serena, Lazzarato, Loretta, and Spyrakis, Francesca

Published
2024
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4. Structure-guided optimization of 3-hydroxybenzoisoxazole derivatives as inhibitors of Aldo-keto reductase 1C3 (AKR1C3) to target prostate cancer

Author

Pippione, Agnese Chiara, Kovachka, Sandra, Vigato, Chiara, Bertarini, Laura, Mannella, Iole, Sainas, Stefano, Rolando, Barbara, Denasio, Enrica, Piercy-Mycock, Helen, Romalho, Linda, Salladini, Edoardo, Adinolfi, Salvatore, Zonari, Daniele, Peraldo-Neia, Caterina, Chiorino, Giovanna, Passoni, Alice, Mirza, Osman Asghar, Frydenvang, Karla, Pors, Klaus, Lolli, Marco Lucio, Spyrakis, Francesca, Oliaro-Bosso, Simonetta, and Boschi, Donatella

Published
2024
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10. Chasing new targets to fight antimicrobial resistance: identification of small molecules affecting the interaction of human hemoglobin with the IsdB hemophore of Staphylococcus aureus

Author

Cozzi, Monica, primary, Failla, Maria Cristina, additional, Gianquinto, Eleonora, additional, Kovachka, Sandra, additional, Buoli Comani, Valeria, additional, Compari, Carlotta, additional, De Bei, Omar, additional, Giaccari, Roberta, additional, Marchesani, Francesco, additional, Marchetti, Marialaura, additional, Ronda, Luca, additional, Rolando, Barbara, additional, Baroni, Massimo, additional, Cruciani, Gabriele, additional, Campanini, Barbara, additional, Bettati, Stefano, additional, Faggiano, Serena, additional, Lazzarato, Loretta, additional, and Spyrakis, Francesca, additional

Published
2024
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11. A community effort in SARS‐CoV‐2 drug discovery

Author

Schimunek, Johannes, primary, Seidl, Philipp, additional, Elez, Katarina, additional, Hempel, Tim, additional, Le, Tuan, additional, Noé, Frank, additional, Olsson, Simon, additional, Raich, Lluís, additional, Winter, Robin, additional, Gokcan, Hatice, additional, Gusev, Filipp, additional, Gutkin, Evgeny M., additional, Isayev, Olexandr, additional, Kurnikova, Maria G., additional, Narangoda, Chamali H., additional, Zubatyuk, Roman, additional, Bosko, Ivan P., additional, Furs, Konstantin V., additional, Karpenko, Anna D., additional, Kornoushenko, Yury V., additional, Shuldau, Mikita, additional, Yushkevich, Artsemi, additional, Benabderrahmane, Mohammed, additional, Bousquet-Melou, Patrick, additional, Bureau, Ronan, additional, Charton, Beatrice, additional, Cirou, Bertrand, additional, Gil, Gérard, additional, Allen, William J., additional, Sirimulla, Suman, additional, Watowich, Stanley, additional, Antonopoulos, Nick, additional, Epitropakis, Nikolaos, additional, Krasoulis, Agamemnon, additional, Pitsikalis, Vassilis, additional, Theodorakis, Stavros, additional, Kozlovskii, Igor, additional, Maliutin, Anton, additional, Medvedev, Alexander, additional, Popov, Petr, additional, Zaretckii, Mark, additional, Eghbal-zadeh, Hamid, additional, Halmich, Christina, additional, Hochreiter, Sepp, additional, Mayr, Andreas, additional, Ruch, Peter, additional, Widrich, Michael, additional, Berenger, Francois, additional, Kumar, Ashutosh, additional, Yamanishi, Yoshihiro, additional, Zhang, Kam, additional, Bengio, Emmanuel, additional, Bengio, Yoshua, additional, Jain, Moksh, additional, Korablyov, Maksym, additional, Liu, Cheng-Hao, additional, Gilles, Marcous, additional, Glaab, Enrico, additional, Barnsley, Kelly, additional, Iyengar, Suhasini M., additional, Ondrechen, Mary Jo, additional, Haupt, V. Joachim, additional, Kaiser, Florian, additional, Schroeder, Michael, additional, Pugliese, Luisa, additional, Albani, Simone, additional, Athanasiou, Christina, additional, Beccari, Andrea, additional, Carloni, Paolo, additional, D'Arrigo, Giulia, additional, Gianquinto, Eleonora, additional, Goßen, Jonas, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Kokh, Daria B., additional, Kovachka, Sandra, additional, Manelfi, Candida, additional, Mukherjee, Goutam, additional, Muñiz-Chicharro, Abraham, additional, Musiani, Francesco, additional, Nunes-Alves, Ariane, additional, Paiardi, Giulia, additional, Rossetti, Giulia, additional, Sadiq, S. Kashif, additional, Spyrakis, Francesca, additional, Talarico, Carmine, additional, Tsengenes, Alexandros, additional, Wade, Rebecca, additional, Copeland, Conner, additional, Gaiser, Jeremiah, additional, Olson, Daniel R., additional, Roy, Amitava, additional, Venkatraman, Vishwesh, additional, Wheeler, Travis J., additional, Arthanari, Haribabu, additional, Blaschitz, Klara, additional, Cespugli, Marco, additional, Durmaz, Vedat, additional, Fackeldey, Konstantin, additional, Fischer, Patrick D., additional, Gorgulla, Christoph, additional, Gruber, Christian, additional, Gruber, Karl, additional, Hetmann, Michael, additional, Kinney, Jamie E., additional, Das, Krishna M. Padmanabha, additional, Pandita, Shreya, additional, Singh, Amit, additional, Steinkellner, Georg, additional, Tesseyre, Guilhem, additional, Wagner, Gerhard, additional, Wang, Zi-Fu, additional, Yust, Ryan J., additional, Druzhilovskiy, Dmitry S., additional, Filimonov, Dmitry, additional, Pogodin, Pavel V., additional, Poroikov, Vladimir, additional, Rudik, Anastassia V., additional, Stolbov, Leonid A., additional, Veselovsky, Alexander V., additional, De Rosa, Maria, additional, Simone, Giada De, additional, Gulotta, Maria R., additional, Lombino, Jessica, additional, Mekni, Nedra, additional, Perricone, Ugo, additional, Casini, Arturo, additional, Embree, Amanda, additional, Gordon, D. Benjamin, additional, Lei, David, additional, Pratt, Katelin, additional, Voigt, Christopher A., additional, Chen, Kuang-Yu, additional, Jacob, Yves, additional, Krischuns, Tim, additional, Lafaye, Pierre, additional, Zettor, Agnès, additional, Rodríguez, M. Luis, additional, White, Kris M., additional, Fearon, Daren, additional, von Delft, Frank, additional, Walsh, Martin A., additional, Horvath, Dragos, additional, Brooks, Charles L., additional, Falsafi, Babak, additional, Ford, Bryan, additional, García-Sastre, Adolfo, additional, Lee, Sang Yup, additional, Naffakh, Nadia, additional, Varnek, Alexandre, additional, Klambauer, Guenter, additional, and Hermans, Thomas M., additional

Published
2023
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12. A community effort to discover small molecule SARS-CoV-2 inhibitors

Author

Schimunek, Johannes, primary, Seidl, Philipp, additional, Elez, Katarina, additional, Hempel, Tim, additional, Le, Tuan, additional, Noé, Frank, additional, Olsson, Simon, additional, Raich, Lluís, additional, Winter, Robin, additional, Gokcan, Hatice, additional, Gusev, Filipp, additional, Gutkin, Evgeny M., additional, Isayev, Olexandr, additional, Kurnikova, Maria G., additional, Narangoda, Chamali H., additional, Zubatyuk, Roman, additional, Bosko, Ivan P., additional, Furs, Konstantin V., additional, Karpenko, Anna D., additional, Kornoushenko, Yury V., additional, Shuldau, Mikita, additional, Yushkevich, Artsemi, additional, Benabderrahmane, Mohammed B., additional, Bousquet-Melou, Patrick, additional, Bureau, Ronan, additional, Charton, Beatrice, additional, Cirou, Bertrand C., additional, Gil, Gérard, additional, Allen, William J., additional, Sirimulla, Suman, additional, Watowich, Stanley, additional, Antonopoulos, Nick A., additional, Epitropakis, Nikolaos E., additional, Krasoulis, Agamemnon K., additional, Pitsikalis, Vassilis P., additional, Theodorakis, Stavros T., additional, Kozlovskii, Igor, additional, Maliutin, Anton, additional, Medvedev, Alexander, additional, Popov, Petr, additional, Zaretckii, Mark, additional, Eghbal-zadeh, Hamid, additional, Halmich, Christina, additional, Hochreiter, Sepp, additional, Mayr, Andreas, additional, Ruch, Peter, additional, Widrich, Michael, additional, Berenger, Francois, additional, Kumar, Ashutosh, additional, Yamanishi, Yoshihiro, additional, Zhang, Kam Y.J., additional, Bengio, Emmanuel, additional, Bengio, Yoshua, additional, Jain, Moksh J., additional, Korablyov, Maksym, additional, Liu, Cheng-Hao, additional, Marcou, Gilles, additional, Glaab, Enrico, additional, Barnsley, Kelly, additional, Iyengar, Suhasini M., additional, Ondrechen, Mary Jo, additional, Haupt, V. Joachim, additional, Kaiser, Florian, additional, Schroeder, Michael, additional, Pugliese, Luisa, additional, Albani, Simone, additional, Athanasiou, Christina, additional, Beccari, Andrea, additional, Carloni, Paolo, additional, D'Arrigo, Giulia, additional, Gianquinto, Eleonora, additional, Goßen, Jonas, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Kokh, Daria B., additional, Kovachka, Sandra, additional, Manelfi, Candida, additional, Mukherjee, Goutam, additional, Muñiz-Chicharro, Abraham, additional, Musiani, Francesco, additional, Nunes-Alves, Ariane, additional, Paiardi, Giulia, additional, Rossetti, Giulia, additional, Sadiq, S. Kashif, additional, Spyrakis, Francesca, additional, Talarico, Carmine, additional, Tsengenes, Alexandros, additional, Wade, Rebecca C., additional, Copeland, Conner, additional, Gaiser, Jeremiah, additional, Olson, Daniel R., additional, Roy, Amitava, additional, Venkatraman, Vishwesh, additional, Wheeler, Travis J., additional, Arthanari, Haribabu, additional, Blaschitz, Klara, additional, Cespugli, Marco, additional, Durmaz, Vedat, additional, Fackeldey, Konstantin, additional, Fischer, Patrick D., additional, Gorgulla, Christoph, additional, Gruber, Christian, additional, Gruber, Karl, additional, Hetmann, Michael, additional, Kinney, Jamie E., additional, Padmanabha Das, Krishna M., additional, Pandita, Shreya, additional, Singh, Amit, additional, Steinkellner, Georg, additional, Tesseyre, Guilhem, additional, Wagner, Gerhard, additional, Wang, Zi-Fu, additional, Yust, Ryan J., additional, Druzhilovskiy, Dmitry S., additional, Filimonov, Dmitry A., additional, Pogodin, Pavel V., additional, Poroikov, Vladimir, additional, Rudik, Anastassia V., additional, Stolbov, Leonid A., additional, Veselovsky, Alexander V., additional, De Rosa, Maria, additional, De Simone, Giada, additional, Gulotta, Maria R., additional, Lombino, Jessica, additional, Mekni, Nedra, additional, Perricone, Ugo, additional, Casini, Arturo, additional, Embree, Amanda, additional, Gordon, D. Benjamin, additional, Lei, David, additional, Pratt, Katelin, additional, Voigt, Christopher A., additional, Chen, Kuang-Yu, additional, Jacob, Yves, additional, Krischuns, Tim, additional, Lafaye, Pierre, additional, Zettor, Agnès, additional, Rodríguez, M. Luis, additional, White, Kris M., additional, Fearon, Daren, additional, Von Delft, Frank, additional, Walsh, Martin A., additional, Horvath, Dragos, additional, Brooks III, Charles L., additional, Falsafi, Babak, additional, Ford, Bryan, additional, García-Sastre, Adolfo, additional, Lee, Sang Yup, additional, Naffakh, Nadia, additional, Varnek, Alexandre, additional, Klambauer, Günter, additional, and Hermans, Thomas M., additional

Published
2023
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14. Investigation into the Use of Encorafenib to Develop Potential PROTACs Directed against BRAFV600E Protein

Author

Marini, Elisabetta, primary, Marino, Marco, additional, Gionfriddo, Giulia, additional, Maione, Federica, additional, Pandini, Marta, additional, Oddo, Daniele, additional, Giorgis, Marta, additional, Rolando, Barbara, additional, Blua, Federica, additional, Gastaldi, Simone, additional, Marchiò, Serena, additional, Kovachka, Sandra, additional, Spyrakis, Francesca, additional, Gianquinto, Eleonora, additional, Di Nicolantonio, Federica, additional, and Bertinaria, Massimo, additional

Published
2022
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15. Investigation into the Use of Encorafenib to Develop Potential PROTACs Directed against BRAF V600E Protein.

Author

Marini, Elisabetta, Marino, Marco, Gionfriddo, Giulia, Maione, Federica, Pandini, Marta, Oddo, Daniele, Giorgis, Marta, Rolando, Barbara, Blua, Federica, Gastaldi, Simone, Marchiò, Serena, Kovachka, Sandra, Spyrakis, Francesca, Gianquinto, Eleonora, Di Nicolantonio, Federica, and Bertinaria, Massimo

Subjects
BRAF genes, SERINE/THREONINE kinases, CELL proliferation, CELL communication, CHEMICAL synthesis, KINASE inhibitors
Abstract

BRAF is a serine/threonine kinase frequently mutated in human cancers. BRAFV600E mutated protein is targeted through the use of kinase inhibitors which are approved for the treatment of melanoma; however, their long-term efficacy is hampered by resistance mechanisms. The PROTAC-induced degradation of BRAFV600E has been proposed as an alternative strategy to avoid the onset of resistance. In this study, we designed a series of compounds where the BRAF kinase inhibitor encorafenib was conjugated to pomalidomide through different linkers. The synthesized compounds maintained their ability to inhibit the kinase activity of mutated BRAF with IC50 values in the 40–88 nM range. Selected compounds inhibited BRAFV600E signaling and cellular proliferation of A375 and Colo205 tumor cell lines. Compounds 10 and 11, the most active of the series, were not able to induce degradation of mutated BRAF. Docking and molecular dynamic studies, conducted in comparison with the efficient BRAF degrader P5B, suggest that a different orientation of the linker bearing the pomalidomide substructure, together with a decreased mobility of the solvent-exposed part of the conjugates, could explain this behavior. [ABSTRACT FROM AUTHOR]

Published
2022
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19. A community effort in SARS‐CoV‐2 drug discovery

Author

Schimunek, Johannes, Seidl, Philipp, Elez, Katarina, Hempel, Tim, Le, Tuan, Noé, Frank, Olsson, Simon, Raich, Lluís, Winter, Robin, Gokcan, Hatice, Gusev, Filipp, Gutkin, Evgeny M., Isayev, Olexandr, Kurnikova, Maria G., Narangoda, Chamali H., Zubatyuk, Roman, Bosko, Ivan P., Furs, Konstantin V., Karpenko, Anna D., Kornoushenko, Yury V., Shuldau, Mikita, Yushkevich, Artsemi, Benabderrahmane, Mohammed B., Bousquet‐Melou, Patrick, Bureau, Ronan, Charton, Beatrice, Cirou, Bertrand C., Gil, Gérard, Allen, William J., Sirimulla, Suman, Watowich, Stanley, Antonopoulos, Nick, Epitropakis, Nikolaos, Krasoulis, Agamemnon, Itsikalis, Vassilis, Theodorakis, Stavros, Kozlovskii, Igor, Maliutin, Anton, Medvedev, Alexander, Popov, Petr, Zaretckii, Mark, Eghbal‐Zadeh, Hamid, Halmich, Christina, Hochreiter, Sepp, Mayr, Andreas, Ruch, Peter, Widrich, Michael, Berenger, Francois, Kumar, Ashutosh, Yamanishi, Yoshihiro, Zhang, Kam Y. J., Bengio, Emmanuel, Bengio, Yoshua, Jain, Moksh J., Korablyov, Maksym, Liu, Cheng‐Hao, Marcou, Gilles, Glaab, Enrico, Barnsley, Kelly, Iyengar, Suhasini M., Ondrechen, Mary Jo, Haupt, V. Joachim, Kaiser, Florian, Schroeder, Michael, Pugliese, Luisa, Albani, Simone, Athanasiou, Christina, Beccari, Andrea, Carloni, Paolo, D'Arrigo, Giulia, Gianquinto, Eleonora, Goßen, Jonas, Hanke, Anton, Joseph, Benjamin P., Kokh, Daria B., Kovachka, Sandra, Manelfi, Candida, Mukherjee, Goutam, Muñiz‐Chicharro, Abraham, Musiani, Francesco, Nunes‐Alves, Ariane, Paiardi, Giulia, Rossetti, Giulia, Sadiq, S. Kashif, Spyrakis, Francesca, Talarico, Carmine, Tsengenes, Alexandros, Wade, Rebecca C., Copeland, Conner, Gaiser, Jeremiah, Olson, Daniel R., Roy, Amitava, Venkatraman, Vishwesh, Wheeler, Travis J., Arthanari, Haribabu, Blaschitz, Klara, Cespugli, Marco, Durmaz, Vedat, Fackeldey, Konstantin, Fischer, Patrick D., Gorgulla, Christoph, Gruber, Christian, Gruber, Karl, Hetmann, Michael, Kinney, Jamie E., Padmanabha Das, Krishna M., Pandita, Shreya, Singh, Amit, Steinkellner, Georg, Tesseyre, Guilhem, Wagner, Gerhard, Wang, Zi‐Fu, Yust, Ryan J., Druzhilovskiy, Dmitry S., Filimonov, Dmitry A., Pogodin, Pavel V., Poroikov, Vladimir, Rudik, Anastassia V., Stolbov, Leonid A., Veselovsky, Alexander V., De Rosa, Maria, De Simone, Giada, Gulotta, Maria R., Lombino, Jessica, Mekni, Nedra, Perricone, Ugo, Casini, Arturo, Embree, Amanda, Gordon, D. Benjamin, Lei, David, Pratt, Katelin, Voigt, Christopher A., Chen, Kuang‐Yu, Jacob, Yves, Krischuns, Tim, Lafaye, Pierre, Zettor, Agnès, Rodríguez, M. Luis, White, Kris M., Fearon, Daren, Von Delft, Frank, Walsh, Martin A., Horvath, Dragos, Brooks, Charles L., Falsafi, Babak, Ford, Bryan, García‐Sastre, Adolfo, Yup Lee, Sang, Naffakh, Nadia, Varnek, Alexandre, Klambauer, Günter, and Hermans, Thomas M.

Abstract

The COVID‐19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availability of vaccines, searching for efficient small‐molecule drugs that are widely available, including in low‐ and middle‐income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the “Billion molecules against COVID‐19 challenge”, to identify small‐molecule inhibitors against SARS‐CoV‐2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find ‘consensus compounds’. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding‐, cleavage‐, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS‐CoV‐2 treatments.

Published
2024
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20. Microscale Thermophoresis to Evaluate the Functionality of Heterologously Overexpressed Membrane Proteins in Membrane Preparations.

Author

Kovachka S, Soule P, and Mus-Veteau I

Subjects
Humans, Protein Binding, Hedgehog Proteins, Membrane Proteins genetics
Abstract

Transmembrane proteins are challenging to express in heterologous systems and to purify, thus any technique enabling to evaluate the functionality of the protein produced prior purification provides a huge step forward. Furthermore, the membrane environment may be critical for the activity of the target protein and accessing information in the membrane fragments instead of solubilizing the target into a detergent that may be unsuitable for its function is key to study and evaluate its activity. Herein, we describe how microscale thermophoresis (MST) was used to evaluate the functionality of membrane proteins directly in host membrane preparation before purification. We give a protocol to measure the affinity between the human Hedgehog (Hh) receptor Ptch1 in yeast plasma membrane and the small molecule PAH, which was shown to inhibit its drug efflux activity., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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