Description: Combining molecular simulations, active learning and experimental validation to discover inhibitors of TMPRSS2. Duration: 2020–2025 Affiliation: Free University of Berlin Role: Research Fellow
Overview
This project focused on discovering inhibitors of TMPRSS2, a host protease required for coronavirus entry. The work progressed from mechanistic studies of TMPRSS2 inhibition (Azouz et al., 2021) and drug repurposing strategies (Hempel et al., 2021)(Hempel et al., 2023), through large-scale community-driven drug discovery efforts (Schimunek et al., 2023), to the development of a screening framework that led to the discovery of a nanomolar inhibitor with broad coronavirus activity (Elez et al., 2025).
Key Contributions
Identified and characterized TMPRSS2 inhibitors with antiviral activity.
Demonstrated synergistic inhibition of SARS-CoV-2 cell entry using drug combinations.
Contributed to a patented pharmaceutical composition for COVID-19 treatment.
Participated in a large-scale open-science drug discovery initiative during the COVID-19 pandemic.
Developed an active-learning framework that reduced computational screening requirements by ~29-fold.
Discovered BMS-262084, a nanomolar inhibitor with broad coronavirus activity.
Background
TMPRSS2 is a host protease required for activation of coronavirus spike proteins and viral entry into human cells. Because it is a host protein rather than a viral target, it represents a promising therapeutic target with reduced risk of resistance from viral mutations. Despite its therapeutic relevance, discovering potent and selective TMPRSS2 inhibitors remains challenging. The protein exhibits conformational flexibility and experimentally screening large compound libraries is costly and time-consuming. These challenges make TMPRSS2 a strong candidate for computational drug discovery approaches that integrate molecular simulations and machine learning to prioritize compounds for experimental testing.
Methodology
Molecular docking
Molecular dynamics simulations
Ensemble-based virtual screening
Active learning
Target-specific scoring function
Experimental validation (biochemical assays and cell-based)
Collaborators
Free University of Berlin: Tim Hempel, Lluís Raich, Robin Winter, Tuan Le, Simon Olsson, Frank Noé
German Primate Center - Leibniz Institute for Primate Research: Nadine Krüger, Nicole Moor, Cheila Rocha, Stefan Pöhlmann, Markus Hoffmann
National Institutes of Health: Jonathan H. Shrimp, Min Shen, Matthew D. Hall
Cincinnati Children’s Hospital Medical Center: Nurit P. Azouz, Marc E. Rothenberg
References
2025
Simulations and active learning enable efficient identification of an experimentally-validated broad coronavirus inhibitor
Katarina Elez, Tim Hempel, Jonathan H. Shrimp, Nicole Moor, Lluís Raich, and 7 more authors
Drug screening resembles finding a needle in a haystack: identifying a few effective inhibitors from a large pool of potential drugs. Large experimental screens are expensive and time-consuming, while virtual screening trades off computational efficiency and experimental correlation. Here we develop a framework that combines molecular dynamics (MD) simulations with active learning. Two components drastically reduce the number of candidates needing experimental testing to less than 20: (1) a target-specific score that evaluates target inhibition and (2) extensive MD simulations to generate a receptor ensemble. The active learning approach reduces the number of compounds requiring experimental testing to less than 10 and cuts computational costs by ∼29-fold. Using this framework, we discovered BMS-262084 as a potent inhibitor of TMPRSS2 (IC50 = 1.82 nM). Cell-based experiments confirmed BMS-262084’s efficacy in blocking entry of various SARS-CoV-2 variants and other coronaviruses. The identified inhibitor holds promise for treating viral and other diseases involving TMPRSS2.
@article{elez_simulations_2025,title={Simulations and active learning enable efficient identification of an experimentally-validated broad coronavirus inhibitor},author={Elez, Katarina and Hempel, Tim and Shrimp, Jonathan H. and Moor, Nicole and Raich, Lluís and Rocha, Cheila and Winter, Robin and Le, Tuan and P\"{o}hlmann, Stefan and Hoffmann, Markus and Hall, Matthew D. and Noé, Frank},year={2025},journal={Nature Communications},volume={16},pages={6949},doi={10.1038/s41467-025-62139-5},altmetric=true,dimensions=true,bibtex_show=true,selected=true}
2023
Pharmaceutical Composition for Treating Covid-19 Comprising Otamixaban and at Least One of Camostat and Nafamostat
Tim Hempel, Katarina Elez, Lluís Raich, Frank Noé, Nadine Krüger, and 2 more authors
The invention relates to a pharmaceutical composition that is appropriate to treat or prevent SARS-CoV-2-related diseases such as COVID-19. The pharmaceutical composition comprises a pharmaceutically effective amount of i) otamixaban or a pharmaceutically acceptable salt thereof and ii) at least one of camostat, a pharmaceutically acceptable salt of camostat, nafamostat, and a pharmaceutically acceptable salt of nafamostat.
@patent{hempel_pharmaceutical_2023,title={Pharmaceutical {{Composition}} for {{Treating Covid-19 Comprising Otamixaban}} and at {{Least One}} of {{Camostat}} and {{Nafamostat}}},author={Hempel, Tim and Elez, Katarina and Raich, Llu{\'i}s and No{\'e}, Frank and Kr{\"u}ger, Nadine and Hoffmann, Markus and P{\"o}hlmann, Stefan},year={2023},number={EP4122461A1},assignee={Freie Universitaet Berlin, Deutsches Primatenzentrum GmbH},note={EP4122461A1},bibtex_show=true,}
A Community Effort in SARS-CoV-2 Drug Discovery
Johannes Schimunek, Philipp Seidl, Katarina Elez, Tim Hempel, Tuan Le, and 147 more authors
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.
@article{schimunek_community_2023,title={A Community Effort in {{SARS-CoV-2}} Drug Discovery},author={Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\'e}, Frank and Olsson, Simon and Raich, Llu{\'i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and {Bousquet-Melou}, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\'e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Pitsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and {Eghbal-Zadeh}, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Go{\ss}en, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and {Mu{\~n}iz-Chicharro}, Abraham and Musiani, Francesco and {Nunes-Alves}, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\'i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and {Garc{\'i}a-Sastre}, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.},year={2023},journal={Molecular Informatics},volume={43},number={1},pages={e202300262},doi={10.1002/minf.202300262},altmetric=true,dimensions=true,bibtex_show=true,}
2021
Alpha 1 Antitrypsin Is an Inhibitor of the SARS-CoV-2–Priming Protease TMPRSS2
Nurit P. Azouz, Andrea Klingler, Victoria Callahan, Ivan Akhrymuk, Katarina Elez, and 7 more authors
Background: Host proteases have been suggested to be crucial for dissemination of MERS, SARS-CoV, and SARS-CoV-2 coronaviruses, but the relative contribution of membrane versus intracellular proteases remains controversial. Transmembrane serine protease 2 (TMPRSS2) is regarded as one of the main proteases implicated in the coronavirus S protein priming, an important step for binding of the S protein to the angiotensin-converting enzyme 2 (ACE2) receptor before cell entry. Methods: We developed a cell-based assay to identify TMPRSS2 inhibitors. Inhibitory activity was established in SARS-CoV-2 viral load systems. Results: We identified the human extracellular serine protease inhibitor (serpin) alpha 1 antitrypsin (A1AT) as a novel TMPRSS2 inhibitor. Structural modeling revealed that A1AT docked to an extracellular domain of TMPRSS2 in a conformation that is suitable for catalysis, resembling similar serine protease inhibitor complexes. Inhibitory activity of A1AT was established in a SARS-CoV-2 viral load system. Notably, plasma A1AT levels were associated with COVID-19 disease severity. Conclusions: Our data support the key role of extracellular serine proteases in SARS CoV-2 infections and indicate that treatment with serpins, particularly the FDA-approved drug A1AT, may be effective in limiting SARS-CoV-2 dissemination by affecting the surface of the host cells.
@article{azouz_alpha_2021,title={Alpha 1 {{Antitrypsin}} Is an {{Inhibitor}} of the {{SARS-CoV-2}}--{{Priming Protease TMPRSS2}}},author={Azouz, Nurit P. and Klingler, Andrea and Callahan, Victoria and Akhrymuk, Ivan and Elez, Katarina and Raich, Llu{\'i}s and Henry, Brandon and Benoit, Justin and Benoit, Stefanie and No{\'e}, Frank and {Kehn-Hall}, Kylene and Rothenberg, Marc},year={2021},journal={Pathogens and Immunity},volume={6},number={1},pages={55--74},doi={10.20411/pai.v6i1.408},altmetric=true,dimensions=true,bibtex_show=true,}
Synergistic Inhibition of SARS-CoV-2 Cell Entry by Otamixaban and Covalent Protease Inhibitors: Pre-Clinical Assessment of Pharmacological and Molecular Properties
Tim Hempel, Katarina Elez, Nadine Krüger, Lluís Raich, Jonathan H. Shrimp, and 8 more authors
SARS-CoV-2, the cause of the COVID-19 pandemic, exploits host cell proteins for viral entry into human lung cells. One of them, the protease TMPRSS2, is required to activate the viral spike protein (S). Even though two inhibitors, camostat and nafamostat, are known to inhibit TMPRSS2 and block cell entry of SARS-CoV-2, finding further potent therapeutic options is still an important task. In this study, we report that a late-stage drug candidate, otamixaban, inhibits SARS-CoV-2 cell entry. We show that otamixaban suppresses TMPRSS2 activity and SARS-CoV-2 infection of a human lung cell line, although with lower potency than camostat or nafamostat. In contrast, otamixaban inhibits SARS-CoV-2 infection of precision cut lung slices with the same potency as camostat. Furthermore, we report that otamixaban’s potency can be significantly enhanced by (sub-) nanomolar nafamostat or camostat supplementation. Dominant molecular TMPRSS2-otamixaban interactions are assessed by extensive 109 μs of atomistic molecular dynamics simulations. Our findings suggest that combinations of otamixaban with supplemental camostat or nafamostat are a promising option for the treatment of COVID-19.
@article{hempel_synergistic_2021,title={Synergistic Inhibition of {{SARS-CoV-2}} Cell Entry by Otamixaban and Covalent Protease Inhibitors: Pre-Clinical Assessment of Pharmacological and Molecular Properties},author={Hempel, Tim and Elez, Katarina and Kr{\"u}ger, Nadine and Raich, Llu{\'i}s and H.~Shrimp, Jonathan and Danov, Olga and Jonigk, Danny and Braun, Armin and Shen, Min and D.~Hall, Matthew and P{\"o}hlmann, Stefan and Hoffmann, Markus and No{\'e}, Frank},year={2021},journal={Chemical Science},volume={12},number={38},pages={12600--12609},publisher={Royal Society of Chemistry},doi={10.1039/D1SC01494C},altmetric=true,dimensions=true,bibtex_show=true,selected=true}
