Optimizing variant-specific therapeutic SARS-CoV-2 decoys using deep-learning-guided molecular dynamics simulations

Autor: Katharina Köchl, Tobias Schopper, Vedat Durmaz, Lena Parigger, Amit Singh, Andreas Krassnigg, Marco Cespugli, Wei Wu, Xiaoli Yang, Yanchong Zhang, Welson Wen-Shang Wang, Crystal Selluski, Tiehan Zhao, Xin Zhang, Caihong Bai, Leon Lin, Yuxiang Hu, Zhiwei Xie, Zaihui Zhang, Jun Yan, Kurt Zatloukal, Karl Gruber, Georg Steinkellner, Christian C. Gruber

Publikováno v: Scientific Reports, Vol 13, Iss 1, Pp 1-15 (2023)

Abstract Treatment of COVID-19 with a soluble version of ACE2 that binds to SARS-CoV-2 virions before they enter host cells is a promising approach, however it needs to be optimized and adapted to emerging viral variants. The computational workflow p

Externí odkaz: https://doaj.org/article/09584ce721704992ad8d2da8bc68bc58

A community effort to discover small molecule SARS-CoV-2 inhibitors

Autor: 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, Thomas M. Hermans

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

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::28010b1a0350f378ef0dcc633e87f6e1
https://doi.org/10.26434/chemrxiv-2023-1d5w8

A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening

Autor: 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

Publikováno v: iScience
iScience, Vol 24, Iss 2, Pp 102021-(2021)
ChemRxiv
article-version (number) 1
article-version (status) pre

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 therap

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::561baa05526285da0be973aafd3b2bc2
https://doi.org/10.26434/chemrxiv.12682316.v1

Functionalization of Enzymatically Synthesized Rigid Poly(itaconate)s via Post-Polymerization aza-Michael Addition of Primary Amines

Autor: Alice Guarneri, Alessandro Pellis, Roberta Vassallo, Fioretta Asaro, Marco Cespugli, Viola Cutifani, Lucia Gardossi, Cynthia Ebert

Publikováno v: Advanced Synthesis and Catalysis 361 (2019) 11
Advanced Synthesis and Catalysis, 361(11), 2559-2573

The bulky 1,4-cyclohexanedimethanol was used as co-monomer for introducing rigidity in lipase synthetized poly(itaconate)s. Poly(1,4-cyclohexanedimethanol itaconate) was synthetized on a 14 g scale at 50 °C, under solvent-free conditions and 70 mbar

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7031f8beb3155a655e053122ade6a9f3
http://hdl.handle.net/11368/2943690

Fully renewable polyesters via polycondensation catalyzed by Thermobifida cellulosilytica cutinase 1: an integrated approach

Autor: Georg M. Guebitz, Enrique Herrero Acero, Lucia Gardossi, Alice Guarneri, Alessandro Pellis, Livia Corici, Valerio Ferrario, Barbara Zartl, Cynthia Ebert, Marco Cespugli

The present study addresses comprehensively the problem of producing polyesters through sustainable processes while using fully renewable raw materials and biocatalysts. Polycondensation of bio-based dimethyl adipate with different diols was catalyze

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::c4721ba78f9749888cdf21a97fa712bb
http://hdl.handle.net/11368/2886133