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4 results on '"Guilhem Tesseyre"'

1. A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening

Author

Christoph Gorgulla, Krishna M. Padmanabha Das, Kendra E. Leigh, Marco Cespugli, Patrick D. Fischer, Zi-Fu Wang, Guilhem Tesseyre, Shreya Pandita, Alec Shnapir, Anthony Calderaio, Minko Gechev, Alexander Rose, Noam Lewis, Colin Hutcheson, Erez Yaffe, Roni Luxenburg, Henry D. Herce, Vedat Durmaz, Thanos D. Halazonetis, Konstantin Fackeldey, J.J. Patten, Alexander Chuprina, Igor Dziuba, Alla Plekhova, Yurii Moroz, Dmytro Radchenko, Olga Tarkhanova, Irina Yavnyuk, Christian Gruber, Ryan Yust, Dave Payne, Anders M. Näär, Mark N. Namchuk, Robert A. Davey, Gerhard Wagner, Jamie Kinney, and Haribabu Arthanari

Subjects
Drugs, High-Performance Computing in Bioinformatics, Structural Biology, Virology, Science
Abstract

Summary: The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics, and targeting multiple points in the viral life cycle could help tackle the current, as well as future, coronaviruses. Here, we leverage our recently developed, ultra-large-scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions.

Published
2021
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3. A community effort to discover small molecule SARS-CoV-2 inhibitors

Author

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

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 a 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 potentially active 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 activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (Nsp12 domain), and (alpha) spike protein S. Overall, 27 potential inhibitors were experimentally confirmed by binding-, cleavage-, and/or viral suppression assays and are presented here. All results are freely available and can be taken further downstream without IP restrictions. Overall, we show the effectiveness of computational techniques, community efforts, and communication across research fields (i.e., protein expression and crystallography, in silico modeling, synthesis and biological assays) to accelerate the early phases of drug discovery.

Published
2023
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4. A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening

Author

Dave Payne, Colin Hutcheson, Alexander Chuprina, Roni Luxenburg, Marco Cespugli, Mark N. Namchuk, Anthony Calderaio, Anders M. Näär, Irina Yavnyuk, Minko Gechev, Gerhard Wagner, Dmytro S. Radchenko, Noam Lewis, Konstantin Fackeldey, Olga Tarkhanova, Vedat Durmaz, Alec Shnapir, Kendra E. Leigh, Alla Plekhova, Shreya Pandita, Ryan Yust, Jamie Kinney, Alexander Rose, Christian Gruber, Robert A. Davey, Krishna Mohan Padmanabha Das, Guilhem Tesseyre, Henry D. Herce, Patrick D. Fischer, Igor Dziuba, J. J. Patten, Haribabu Arthanari, Zi-Fu Wang, Christoph Gorgulla, Thanos D. Halazonetis, Yurii S. Moroz, Erez Yaffe, Leigh, Kendra [0000-0002-6467-3330], and Apollo - University of Cambridge Repository

Subjects
0301 basic medicine, 2019-20 coronavirus outbreak, structure-based virtual screening, Coronavirus disease 2019 (COVID-19), Computer science, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), viruses, In silico, coronavirus, in silico screening, Cloud computing, 02 engineering and technology, Computational biology, medicine.disease_cause, Article, drug discovery, 03 medical and health sciences, Viral life cycle, Structural Biology, Virology, Global health, medicine, lcsh:Science, Coronavirus, Virtual screening, Multidisciplinary, SARS-CoV-2, Drug discovery, business.industry, COVID-19, Drugs, 021001 nanoscience & nanotechnology, Small-molecule inhibitors, 030104 developmental biology, Drug development, lcsh:Q, 0210 nano-technology, business, High-Performance Computing in Bioinformatics
Abstract

The unparalleled global effort to combat the continuing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic over the last year has resulted in promising prophylactic measures. However, a need still exists for cheap, effective therapeutics and targeting multiple points in the viral life cycle could help tackle the current as well as future coronaviruses. Here we leverage our recently developed, ultra-large scale in silico screening platform, VirtualFlow, to search for inhibitors that target SARS-CoV-2. In this unprecedented structure-based virtual campaign, we screened roughly 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets. In addition to targeting the active sites of viral enzymes, we also targeted critical auxiliary sites such as functionally important protein-protein interactions., Graphical Abstract, Highlights • Ultra-large in silico screen of targets important for the replication of SARS-CoV-2 (85) • Screening of multiple functional sites on individual target proteins (70) • 17 target proteins, 45 screens, ∼50 billion docking instances to target SARS-CoV-2 (84) • Conservation in some target sites means hits could exhibit pan-coronavirus function (85)

Published
2020
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