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1. Gluebodies improve crystal reliability and diversity through transferable nanobody mutations that introduce constitutive crystal contacts

Author

Mingda Ye, Mpho Makola, Joseph A. Newman, Michael Fairhead, Elizabeth Maclean, Nathan D. Wright, Lizbé Koekemoer, Andrew Thompson, Gustavo A. Bezerra, Gangshun Yi, Huanyu Li, Victor L. Rangel, Dimitrios Mamalis, Hazel Aitkenhead, Benjamin G. Davis, Robert J.C. Gilbert, Katharina Duerr, Opher Gileadi, and Frank von Delft

Abstract

Obtaining protein crystals suitable for characterizing ligands and understanding different protein conformations remains a bottleneck for structural studies. Using nanobodies as crystallization chaperones is one strategy to address the problem, but its reliability is uncharacterized and in this study, we observed it to have a poor success rate. We therefore set out to engineer robust crystallization behaviour into the nanobody scaffold by exploring the nanobody-nanobody interface predominant in the PDB using >200 combinations of surface mutations. This yielded multiple polymorphs, all mediated by this interface, with one providing far superior resolution and reliability of diffraction. We therefore refer to the modified nanobody scaffolds as “Gluebodies” and propose at least 2 variants that should be routinely generated for chaperone experiments. We furthermore show that Gluedodies cannot rescue intrinsically non-crystallizing proteins, but are a powerful approach to improve the packing and resolution limit of poorly diffracting crystals.

Published
2022
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2. COVID Moonshot: Open Science Discovery of SARS-CoV-2 Main Protease Inhibitors by Combining Crowdsourcing, High-Throughput Experiments, Computational Simulations, and Machine Learning

Author

Anna Carbery, Annette von Delft, Boris Kovar, Vishwanath Swamy, Ronen Gabizon, Nathan Wright, Charlie Weatherall, Susana Tomasio, Hannah E. Bruce Macdonald, Daniel Zaidmann, Ailsa Powell, P. Gehrtz, Noam Erez, Walter Ward, Vladimir Psenak, Finny S. Varghese, Edward J Griffen, Halina Mikolajek, Sharon Melamed, Emma Cattermole, A. Aimon, Elad Bar-David, Louise Dunnett, Maneesh Pingle, Warren Thompson, Efrat Resnick, William G. Glass, Mark Daniel Calmiano, J. L. Kiappes, Lizbe Koekemoer, Mariana Vaschetto, Andrew Jajack, Nir London, Martin Walsh, Beth MacLean, Charline Giroud, Haim Levy, Anastassia L. Kantsadi, Vladas Oleinikovas, Andrew Thompson, Vincent A. Voelz, Assa Sittner, Tomer Israely, John Spencer, Itai Glinert, Matthew F. D. Hurley, Richard Foster, T.J. Gorrie-Stone, Aarif Shaikh, Gijs J. Overheul, Conor Francis Wild, Michael Fairhead, Benjamin Ian Perry, David Owen, Michelle L. Hill, Peter W. Kenny, Sarma Bvnbs, Galit Cohen, Ralph P. Robinson, Jakir Pinjari, Carina Gileadi, Amir Ben-Shmuel, Shay Weiss, Victor L. Rangel, Matthew C. Robinson, Anthony Tumber, D. Fearon, Jag Paul Heer, Boaz Politi, Nicole Zitzmann, Claire Strain-Damerell, Tika R. Malla, Oleg M. Michurin, Peter K. Eastman, Christopher J. Schofield, Matthew Wittmann, Jin Pan, Eric Jnoff, Shirly Duberstein, Mihaela D. Smilova, Haim Barr, Ronald P. van Rij, Joseph E. Coffland, Garrett M. Morris, Austin Clyde, Khriesto A. Shurrush, Einat B. Vitner, Ruby Pai, Alessandro Contini, St Patrick Reid, Jose Brandao Neto, Lisa Cox, Tatiana Matviiuk, Jiye Shi, Sam Horrell, Ioannis Vakonakis, Aaron Morris, Hadeer Zidane, Juliane Brun, Yfat Yahalom-Ronen, Hadas Tamir, R. Skyner, Tobias John, John D. Chodera, Nir Paran, Alex Dias, Dominic Rufa, Willam McCorkindale, Reut Puni, Hagit Achdout, Rachael Tennant, Holly Foster, Tim Dudgeon, Bruce A. Lefker, Rambabu N. Reddi, Marian V. Gorichko, Frank von Delft, Alpha A. Lee, Milan Cvitkovic, T. Krojer, Demetri Moustakas, Oleg Fedorov, Robert C. Glen, Jason C. Cole, Petra Lukacik, Matteo P. Ferla, Melissa L Bobby, Adam Smalley, Jim Bennett, Melody Jane Morwitzer, and Alice Douangamath

Subjects
Open science, Protease, Computer science, business.industry, Drug discovery, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), medicine.medical_treatment, Crowdsourcing, Machine learning, computer.software_genre, Enzymatic Assays, medicine, Ic50 values, Artificial intelligence, business, Throughput (business), computer
Abstract

Herein we provide a living summary of the data generated during the COVID Moonshot project focused on the development of SARS-CoV-2 main protease (Mpro) inhibitors. Our approach uniquely combines crowdsourced medicinal chemistry insights with high throughput crystallography, exascale computational chemistry infrastructure for simulations, and machine learning in triaging designs and predicting synthetic routes. This manuscript describes our methodologies leading to both covalent and non-covalent inhibitors displaying protease IC50 values under 150 nM and viral inhibition under 5 uM in multiple different viral replication assays. Furthermore, we provide over 200 crystal structures of fragment-like and lead-like molecules in complex with the main protease. Over 1000 synthesized and ordered compounds are also reported with the corresponding activity in Mpro enzymatic assays using two different experimental setups. The data referenced in this document will be continually updated to reflect the current experimental progress of the COVID Moonshot project, and serves as a citable reference for ensuing publications. All of the generated data is open to other researchers who may find it of use.

Published
2020
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3. Open Science Discovery of Potent Non-Covalent SARS-CoV-2 Main Protease Inhibitors

Author

von Delft F, Ronen Gabizon, Wild Cf, Anastassia L. Kantsadi, Peter W. Kenny, Koekemoer L, Matteo P. Ferla, Noam Erez, Sharon Melamed, Adam Smalley, Gijs J. Overheul, Jag Paul Heer, Shaikh A, Tika R. Malla, R.S. Fernandes, Christopher J. Schofield, Moustakas D, Pai R, MacLean B, T. Krojer, Finny S. Varghese, Elad Bar-David, Hagit Achdout, Gregory R. Bowman, Lefker Ba, Kovar B, Charlie Weatherall, Tennant R, Griffen Ej, Yfat Yahalom-Ronen, Louise Dunnett, Emma Cattermole, Bvnbs S, Chernyshenko E, Ripka Eg, Kim Donckers, Efrat Resnick, Nir Paran, J. L. Kiappes, Einat B. Vitner, Dotson Dl, Mark Daniel Calmiano, Juliane Brun, Victor L. Rangel, Matthew F. D. Hurley, Richard Foster, Garrett M. Morris, Vaschetto M, Austin Clyde, Shay Weiss, Pan J, Nir London, William McCorkindale, Dudgeon T, Martin A. Walsh, Borden B, Haim Barr, John Spencer, Zaidmann D, Alice Douangamath, Robinson Rp, Alexandre Dias, John D. Chodera, Morris A, Marian V. Gorichko, Oleg Fedorov, V.O. Gawriljuk, Petra Lukacik, Puni R, Pinjari J, Shafeev M, Dirk Jochmans, Assa Sittner, T.J. Gorrie-Stone, White Km, Amir Ben-Shmuel, Ioannis Vakonakis, Boaz Politi, Rambabu N. Reddi, Joseph E. Coffland, Itai Glinert, Matthew C. Robinson, Ferrins L, Tomasio S, Alpha A. Lee, Khriesto A. Shurrush, Holly Foster, A. Aimon, Boby Ml, Andrea Volkamer, Alessandro Contini, Voelz, Tobias John, Galit Cohen, A.M. Nakamura, Horrell S, G.D. Noske, Jim Bennett, Oleg M. Michurin, Nicholas A. Wright, Smilova, von Delft A, Ward W, Haim Levy, Tomer Israely, Fate G, McGovern Bl, Anna Carbery, David R. Owen, Zidane H, Cox L, Michael Fairhead, Psenak, Carina Gileadi, Wittmann M, Morwitzer Mj, Solmesky Lj, Anthony Tumber, Robert C. Glen, Eric Jnoff, Reid Sp, Sukrit Singh, Steven De Jonghe, Claire Strain-Damerell, Jason C. Cole, A.J. Powell, Rosales R, Nicole Zitzmann, D. Fearon, Nguyen L, Rodriguez-Guerra J, Shirly Duberstein, Andrew Thompson, Johan Neyts, Benjamin Ian Perry, van Rij Rp, Jose Brandao Neto, William G. Glass, Rufa D, Charline Giroud, Peter Eastman, Hannah E. Bruce Macdonald, Glaucius Oliva, Mark A. Hill, Laura Vangeel, Jiye Shi, Hadas Tamir, R. Skyner, Mikolajek H, Adolfo García-Sastre, Oleinikovas, Pingle M, Henry M, Cvitkovic M, Milne Bf, Hart Sh, Eyermann Cj, Thompson W, Matviiuk T, Andre S. Godoy, Swamy, P. Gehrtz, and Jajack A

Subjects
Open science, Open knowledge, Protease, Structural biology, Drug discovery, Computer science, Non covalent, Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), medicine.medical_treatment, medicine, Protease inhibitor (pharmacology), Computational biology
Abstract

The COVID-19 pandemic was a stark reminder that a barren global antiviral pipeline has grave humanitarian consequences. Pandemics could be prevented in principle by accessible, easily deployable broad-spectrum oral antivirals. Here we report the results of theCOVID Moonshot, a fully open-science, crowd sourced, structure-enabled drug discovery campaign targeting the SARS-CoV-2 main protease. We discovered a novel chemical series that is differentiated from current Mpro inhibitors in that it maintains a new non-covalent, non-peptidic scaffold with nanomolar potency. Our approach leveraged crowdsourcing, high-throughput structural biology, machine learning, and exascale molecular simulations and high-throughput chemistry. In the process, we generated a detailed map of the structural plasticity of the SARS-CoV-2 main protease, extensive structure-activity relationships for multiple chemotypes, and a wealth of biochemical activity data. In a first for a structure-based drug discovery campaign, all compound designs (>18,000 designs), crystallographic data (>840 ligand-bound X-ray structures), assay data (>10,000 measurements), and synthesized molecules (>2,400 compounds) for this campaign were shared rapidly and openly, creating a rich open and IP-free knowledgebase for future anti-coronavirus drug discovery.

Published
2020
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4. SARS-CoV-2 infects the human kidney and drives fibrosis in kidney organoids

Author

Jitske Jansen, Katharina C. Reimer, James S. Nagai, Finny S. Varghese, Gijs J. Overheul, Marit de Beer, Rona Roverts, Deniz Daviran, Liline A.S. Fermin, Brigith Willemsen, Marcel Beukenboom, Sonja Djudjaj, Saskia von Stillfried, Larissa E. van Eijk, Mirjam Mastik, Marian Bulthuis, Wilfred den Dunnen, Harry van Goor, Jan-Luuk Hillebrands, Sergio H. Triana, Theodore Alexandrov, Marie-Cherelle Timm, Bartholomeus T. van den Berge, Martijn van den Broek, Quincy Nlandu, Joelle Heijnert, Eric M.J. Bindels, Remco M. Hoogenboezem, Fieke Mooren, Christoph Kuppe, Pascal Miesen, Katrien Grünberg, Ties Ijzermans, Eric J. Steenbergen, Jan Czogalla, Michiel F. Schreuder, Nico Sommerdijk, Anat Akiva, Peter Boor, Victor G. Puelles, Jürgen Floege, Tobias B. Huber, Ronald P. van Rij, Ivan G. Costa, Rebekka K. Schneider, Bart Smeets, Rafael Kramann, Hagit Achdout, Anthony Aimon, Elad Bar-David, Haim Barr, Amir Ben-Shmuel, James Bennett, Melissa L. Boby, Bruce Borden, Gregory R. Bowman, Juliane Brun, Sarma BVNBS, Mark Calmiano, Anna Carbery, Emma Cattermole, Eugene Chernychenko, John D. Choder, Austin Clyde, Joseph E. Coffland, Galit Cohen, Jason Cole, Alessandro Contini, Lisa Cox, Milan Cvitkovic, Alex Dias, Kim Donckers, David L. Dotson, Alica Douangamath, Shirly Duberstein, Tim Dudgeon, Louise Dunnett, Peter K. Eastman, Noam Erez, Charles J. Eyermann, Mike Fairhead, Gwen Fate, Daren Fearon, Oleg Federov, Matteo Ferla, Rafaela S. Fernandes, Lori Ferrins, Richard Foster, Holly Foster, Ronen Gabizon, Adolfo Garcia-Sastre, Victor O. Gawriljuk, Paul Gehrtz, Carina Gileadi, Charline Giroud, William G. Glass, Robert Glen, null Itai glinert, Andre S. Godoy, Marian Gorichko, Tyler Gorrie-Stone, Ed J. Griffen, Storm Hassell Hart, Jag Heer, Micheal Henry, Michelle Hill, Sam Horrell, Matthew F.D. Hurley, Tomer Israely, Andrew Jajack, Eric Jnoff, Dirk Jochmans, Tobias John, Steven De Jonghe, Anastassia L. Kantsadi, Peter W. Kenny, J.L. Kiappes, Lizbe Koekemoer, Boris Kovar, Tobias Krojer, Alpha A. Lee, Bruce A. Lefker, Haim Levy, Nir London, Petra Lukacik, Hannah Bruce Macdonald, Beth Maclean, Tika R. Malla, Tatiana Matviiuk, Willam McCorkindale, Briana L. McGovern, Sharon Melamed, Oleg Michurin, Halina Mikolajek, Bruce F. Milne, Aaron Morris, Garret M. Morris, Melody Jane Morwitzer, Demetri Moustakas, Aline M. Nakamura, Jose Brandao Neto, Johan Neyts, Luong Nguyen, Gabriela D. Noske, Vladas Oleinikovas, Glaucius Oliva, David Owen, Vladimir Psenak, Ruby Pai, Jin Pan, Nir Paran, Benjamin Perry, Maneesh Pingle, Jakir Pinjari, Boaz Politi, Ailsa Powell, Reut Puni, Victor L. Rangel, Ranbabu N. Reddi, St Patrick Reid, Efrat Resnick, Emily Grace Ripka, Matthew C. Robinson, Ralph P. Robinson, Jaime Rodriguez-Guerra, Romel Rosales, Dominic Rufa, Chris Schofield, Mikhail Shafeev, Aarif Shaikh, Jiye Shi, Khriesto Shurrush, Sukrit Sing, Assa Sittner, Rachael Skyner, Adam Smalley, Mihaela D. Smilova, Leonardo J. Solmesky, John Spencer, Claire Strain-Damarell, Vishwanath Swamy, Hadas Tamir, Rachael Tennant, Warren Thompson, Andrew Thompson, Susana Tomasia, Anthony Tumber, Ioannis Vakonakis, Laura van Geel, Mariana Vaschetto, Einat B. Vitner, Vincent Voelz, Andra Volkamer, Frank von Delft, Annette von Delft, Martin Walsh, Walter Ward, Charlie Weatherall, Shay Weiss, Kris M. White, Conor Francis Wild, Matthew Wittmann, Nathan Wright, Yfat Yahalom-Ronen, Daniel Zaidmann, Hadeer Zidane, Nicole Zitzmann, Hematology, Developmental Biology, Internal Medicine, Molecular Neuroscience and Ageing Research (MOLAR), Groningen Institute for Organ Transplantation (GIOT), and Groningen Kidney Center (GKC)

Subjects
FÍGADO, viruses, lnfectious Diseases and Global Health Radboud Institute for Molecular Life Sciences [Radboudumc 4], Rare cancers Radboud Institute for Molecular Life Sciences [Radboudumc 9], Kidney, All institutes and research themes of the Radboud University Medical Center, Post-Acute COVID-19 Syndrome, SDG 3 - Good Health and Well-being, Urological cancers Radboud Institute for Molecular Life Sciences [Radboudumc 15], Genetics, Humans, SARS-CoV-2, human iPSC kidney organoids, fibrosis, fungi, COVID-19, Cell Biology, Clinical and Translational Report, Fibrosis, Organoids, Reconstructive and regenerative medicine Radboud Institute for Molecular Life Sciences [Radboudumc 10], Renal disorders Radboud Institute for Molecular Life Sciences [Radboudumc 11], kidney injury, Molecular Medicine, protease blocker, Nanomedicine Radboud Institute for Molecular Life Sciences [Radboudumc 19], chronic kidney disease
Abstract

Kidney failure is frequently observed during and after COVID-19, but it remains elusive whether this is a direct effect of the virus. Here, we report that SARS-CoV-2 directly infects kidney cells and is associated with increased tubule-interstitial kidney fibrosis in patient autopsy samples. To study direct effects of the virus on the kidney independent of systemic effects of COVID-19, we infected human induced pluripotent stem cell-derived kidney organoids with SARS-CoV-2. Single cell RNA-sequencing indicated injury and dedifferentiation of infected cells with activation of pro-fibrotic signaling pathways. Importantly, SARS-CoV-2 infection also led to increased collagen 1 protein expression in organoids. A SARS-CoV-2 protease inhibitor was able to ameliorate the infection of kidney cells by SARS-CoV-2. Our results suggest that SARS-CoV-2 can directly infect kidney cells and induce cell injury with subsequent fibrosis. These data could explain both acute kidney injury in COVID-19 patients and the development of chronic kidney disease in Long-COVID., Graphical Abstract, Jansen, Reimer, Nagai et al report that SARS-CoV-2 infects kidney cells and is associated with kidney fibrosis in patients. Using single cell transcriptomics of infected kidney organoids, they show that SARS-CoV-2 causes kidney injury and stimulates pro-fibrotic signaling. Viral infection in organoids was inhibited by a recently developed protease blocker.

Published
2022

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