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1. 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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2. 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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4. Biophysical characterization of calcium-binding and modulatory-domain dynamics in a pentameric ligand-gated ion channel

Author

Lycksell, Marie, Rovšnik, Urška, Hanke, Anton, Martel, Anne, Howard, Rebecca J., Lindahl, Erik, Lycksell, Marie, Rovšnik, Urška, Hanke, Anton, Martel, Anne, Howard, Rebecca J., and Lindahl, Erik

Abstract

Pentameric ligand-gated ion channels (pLGICs) perform electrochemical signal transduction in organisms ranging from bacteria to humans. Among the prokaryotic pLGICs, there is architectural diversity involving N-terminal domains (NTDs) not found in eukaryotic relatives, exemplified by the calcium-sensitive channel (DeCLIC) from a Desulfofustis deltaproteobacterium, which has an NTD in addition to the canonical pLGIC structure. Here, we have characterized the structure and dynamics of DeCLIC through cryoelectron microscopy (cryo-EM), small-angle neutron scattering (SANS), and molecular dynamics (MD) simulations. In the presence and absence of calcium, cryo-EM yielded structures with alternative conformations of the calcium-binding site. SANS profiles further revealed conformational diversity at room temperature beyond that observed in static structures, shown through MD to be largely attributable to rigid-body motions of the NTD relative to the protein core, with expanded and asymmetric conformations improving the fit of the SANS data. This work reveals the range of motion available to the DeCLIC NTD and calcium-binding site, expanding the conformational landscape of the pLGIC family. Further, these findings demonstrate the power of combining low-resolution scattering, high-resolution structural, and MD simulation data to elucidate interfacial interactions that are highly conserved in the pLGIC family.

Published
2022
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6. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics

Author

Gossen, Jonas, Albani, Simone, Hanke, Anton, Joseph, Benjamin P., Bergh, Cathrine, Kuzikov, Maria, Costanzi, Elisa, Manelfi, Candida, Storici, Paola, Gribbon, Philip, Beccari, Andrea R., Talarico, Carmine, Spyrakis, Francesca, Lindahl, Erik, Zaliani, Andrea, Carloni, Paolo, Wade, Rebecca C., Musiani, Francesco, Kokh, Daria B., Rossetti, Giulia, Gossen, Jonas, Albani, Simone, Hanke, Anton, Joseph, Benjamin P., Bergh, Cathrine, Kuzikov, Maria, Costanzi, Elisa, Manelfi, Candida, Storici, Paola, Gribbon, Philip, Beccari, Andrea R., Talarico, Carmine, Spyrakis, Francesca, Lindahl, Erik, Zaliani, Andrea, Carloni, Paolo, Wade, Rebecca C., Musiani, Francesco, Kokh, Daria B., and Rossetti, Giulia

Abstract

The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of similar to 30 000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing similar to 200 virtual screenings of compound libraries on selected protein structures, we redefine the protein's druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites., QC 20210719

Published
2021
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7. Structural characterization of an Arf dimer interface: molecular mechanism of Arf-dependent membrane scission

Author

Diestelkoetter-Bachert, Petra, Beck, Rainer, Reckmann, Inge, Hellwig, Andrea, Garcia-Saez, Ana, Zelman-Hopf, Monika, Hanke, Anton, Alves, Ariane Nunes, Wade, Rebecca C., Mayer, Matthias P., Wieland, Felix, Diestelkoetter-Bachert, Petra, Beck, Rainer, Reckmann, Inge, Hellwig, Andrea, Garcia-Saez, Ana, Zelman-Hopf, Monika, Hanke, Anton, Alves, Ariane Nunes, Wade, Rebecca C., Mayer, Matthias P., and Wieland, Felix

Abstract

Dimerization of the small GTPase Arf is prerequisite for the scission of COPI-coated transport vesicles. Here, we quantify the monomer/dimer equilibrium of Arf within the membrane and show that after membrane scission, Arf dimers are restricted to donor membranes. By hydrogen exchange mass spectrometry, we define the interface of activated dimeric Arf within its switch II region. Single amino acid exchanges in this region reduce the propensity of Arf to dimerize. We suggest a mechanism of membrane scission by which the dimeric form of Arf is segregated to the donor membrane. Our data are consistent with the previously reported absence of dimerized Arf in COPI vesicles and could explain the presence of one single scar-like noncoated region in each COPI vesicle.

Published
2020

8. A Blueprint for High Affinity SARS-CoV-2 Mpro Inhibitors from Activity-Based Compound Library Screening Guided by Analysis of Protein Dynamics

Author

Gossen, Jonas, primary, Albani, Simone, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Bergh, Cathrine, additional, Kuzikov, Maria, additional, Costanzi, Elisa, additional, Manelfi, Candida, additional, Storici, Paola, additional, Gribbon, Philip, additional, Beccari, Andrea R., additional, Talarico, Carmine, additional, Spyrakis, Francesca, additional, Lindahl, Erik, additional, Zaliani, Andrea, additional, Carloni, Paolo, additional, Wade, Rebecca C., additional, Musiani, Francesco, additional, Kokh, Daria B., additional, and Rossetti, Giulia, additional

Published
2021
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9. A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

Author

Gossen, Jonas, primary, Albani, Simone, additional, Hanke, Anton, additional, Joseph, Benjamin P., additional, Bergh, Cathrine, additional, Kuzikov, Maria, additional, Costanzi, Elisa, additional, Manelfi, Candida, additional, Storici, Paola, additional, Gribbon, Philip, additional, Beccari, Andrea R., additional, Talarico, Carmine, additional, Spyrakis, Francesca, additional, Lindahl, Erik, additional, Zaliani, Andrea, additional, Carloni, Paolo, additional, Wade, Rebecca C., additional, Musiani, Francesco, additional, Kokh, Daria B., additional, and Rossetti, Giulia, additional

Published
2020
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10. Structural characterization of an Arf dimer interface: molecular mechanism of Arf‐dependent membrane scission

Author

Diestelkoetter‐Bachert, Petra, primary, Beck, Rainer, additional, Reckmann, Inge, additional, Hellwig, Andrea, additional, Garcia‐Saez, Ana, additional, Zelman‐Hopf, Monika, additional, Hanke, Anton, additional, Nunes Alves, Ariane, additional, Wade, Rebecca C., additional, Mayer, Matthias P., additional, and Wieland, Felix, additional

Published
2020
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11. 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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