Scientific Publications

30. Fan Bu, Gang Ye, Hailey Turner-Hubbard, Morgan Herbst, Bin Liu & Fang Li. Cryo-EM structure of Sudan ebolavirus glycoprotein complexed with its human endosomal receptor NPC1. Commun Biol 8, 156 (2025). https://doi.org/10.1038/s42003-025-07613-y

29. Jie Li, Oufan Zhang, Kunyang Sun, Yingze Wang, Xingyi Guan, Dorian Bagni, Mojtaba Haghighatlari, Fiona L. Kearns, Conor Parks, Rommie E. Amaro, and Teresa Head-Gordon. Mining for Potent Inhibitors through Artificial Intelligence and Physics: A Unified Methodology for Ligand Based and Structure Based Drug Design. Journal of Chemical Information and Modeling 2024 64 (24), 9082-9097 DOI: 10.1021/acs.jcim.4c00634

28. Fan Bu, Gang Ye, Kimberly Morsheimer, Alise Mendoza, Hailey Turner-Hubbard, Morgan Herbst, Benjamin Spiller, Brian E. Wadzinski, Brett Eaton, Manu Anantpadma, Ge Yang, Bin Lui, Robert Davey, Fang Li. (2024) Discovery of Nanosota-EB1 and -EB2 as Novel Nanobody Inhibitors Against Ebola Virus Infection. PLoS Pathog 20(12): e1012817. https://doi.org/10.1371/journal.ppat.1012817

27. Malaika D. Argade, Jazmin Galván Achi, Ryan Bott, Kimberly M. Morsheimer, Callum D. Owen, Christian A. Zielinski, Arsen M. Gaisin, Mario Alvarez, Terry W. Moore, Fan Bu, Fang Li, Michael Cameron, Manu Anantpadma, Robert A. Davey, Norton P. Peet, Lijun Rong, and Irina N. Gaisina. Guardians at the Gate: Optimization of Small Molecule Entry Inhibitors of Ebola and Marburg Viruses. Journal of Medicinal Chemistry. 2024 Nov: DOI: 10.1021/acs.jmedchem.4c01646

26. Morgan A Esler, Christopher A Belica, Joseph A Rollie, William L Brown, Seyed Arad Moghadasi, Ke Shi, Daniel A Harki, Reuben S Harris, Hideki Aihara, A compact stem-loop DNA aptamer targets a uracil-binding pocket in the SARS-CoV-2 nucleocapsid RNA-binding domain, Nucleic Acids Research, Volume 52, Issue 21, 27 November 2024, Pages 13138–13151, https://doi.org/10.1093/nar/gkae874

25. Gang Ye, Fan Bu, Divyasha Saxena, Hailey Turner-Hubbard, Morgan Herbst, Benjamin Spiller, Brian E. Wadzinski, Lanying Du, Bin Liu, Jian Zheng, Fang Li (2024). Discovery of Nanosota-9 as anti-Omicron nanobody therapeutic candidate. PLoS Pathog 20(11): e1012726: https://doi.org/10.1371/journal.ppat.1012726

24. Gang Ye, Fan Bu, Ruangang Pan, Alise Mendoza, Ge Yang, Benjamin Spiller, Brian E. Wadzinski, Lanying Du, Stanley Perlman, Bin Liu, Fang Li. (2024) Structure-guided in vitro evolution of nanobodies targeting new viral variants. PLoS Pathog 20(9): e1012600. https://doi.org/10.1371/journal.ppat.1012600

23. Gang Ye, Fan Bu, Ruangang Pan, Alise Mendoza, Divyasha Saxena, Jian Zheng, Stanley Perlman, Bin Liu, Fang Li. (2024) Dual-role epitope on SARS-CoV-2 spike enhances and neutralizes viral entry across different variants. PLoS Pathog 20(9): e1012493. https://doi.org/10.1371/journal.ppat.1012493

22. Yuka Otsuka, Lizhou Zhang, Huihui Mou, Justin Shumate, Claire E Kitzmiller, Louis Scampavia, Thomas D Bannister, Michael Farzan, Hyeryun Choe, Timothy P Spicer (2024). Simultaneous screening for selective SARS-CoV-2, Lassa, and Machupo virus entry inhibitors. SLAS discovery : advancing life sciences R & D29(6), 100178. https://doi.org/10.1016/j.slasd.2024.100178

21. Yuka Otsuka, Eunjung Kim, Austin Krueger, Justin Shumate, Chao Wang, Bilel Bdiri, Sultan Ullah, HaJeung Park, Louis Scampavia, Thomas D Bannister, Donghoon Chung, Timothy P Spicer 4 (2024). High throughput screening for SARS-CoV-2 helicase inhibitors. SLAS discovery : advancing life sciences R & D29(6), 100180. https://doi.org/10.1016/j.slasd.2024.100180

20. Renee Delgado, Jyoti Vishwakarma, Seyed Arad Moghadasi, Yuka Otsuka, Justin Shumate, Ashley Cuell, Megan Tansiongco, Christina B. Cooley, Yanjun Chen, Agnieszka Dabrowska,  Rahul Basu, Paulina Duhita Anindita,  Dahai Luo, Peter I. Dosa, Daniel A. Harki, Thomas Bannister, Louis Scampavia, Timothy P. Spicer, Reuben S. Harris (2024). SARS-CoV-2 Mpro inhibitor identification using a cellular gain-of-signal assay for high-throughput screening. SLAS discovery : advancing life sciences R & D, 100181. Advance online publication. https://doi.org/10.1016/j.slasd.2024.100181

19. Paulina Duhita Anindita, Yuka Otsuka, Simon Lattmann, Khac Huy Ngo, Chong Wai Liew, CongBao Kang, Reuben S. Harris, Louis Scampavia, Timothy P. Spicer, Dahai Luo; A high-throughput cell-based screening method for Zika virus protease inhibitor discovery; SLAS Discovery, Volume 29, Issue 5, 100164; PMID: 38796112 DOI: 10.1016/j.slasd.2024.100164

18. Yang Yang, Fang Li, Lanying Du. Therapeutic nanobodies against SARS-CoV-2 and other pathogenic human coronaviruses. J Nanobiotechnology. 2024;22(1):304. Published 2024 May 31. PMID: 38822339 PMCID: PMC11140877 DOI: 10.1186/s12951-024-02573-7

17. Jie Li, Xingyi Guan, Oufan Zhang, Kunyang Sun, Yingze Wang, Dorian Bagni, Teresa Head-Gordon. Leak Proof PDBBind: A Reorganized Dataset of Protein-Ligand Complexes for More Generalizable Binding Affinity Prediction. Preprint. ArXiv. 2024;arXiv:2308.09639v2. Published 2024 May 3. PMID: 37645037 PMCID: PMC10462179

16. Qibin Geng, Yushun Wan, Fu-Chun Hsueh, Jian Shang, Gang Ye, Fan Bu, Morgan Herbst, Rowan Wilkens, Bin Liu, Fang Li (2023) Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein eLife https://doi.org/10.7554/eLife.74060

15. Hinh Ly (2023) The ever-expanding diversity and complexity of the Arenaviridae family, Virulence, 14:1, DOI: 10.1080/21505594.2023.2279353

14. Gang Ye, Ruangang Pan, Fan Bu, Jian Zheng, Alise Mendoza, Wei Wen, Lanying Du, Benjamin Spiller, Brian E. Wadzinski, Bin Liu, Stanley Perlman, Fang Li. Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19. J Virol. 2023 Oct 19:e0144823. doi: 10.1128/jvi.01448-23. PMID: 37855638.

13. Francesco Costacurta, Andrea Dodaro, David Bante, Helge Schöppe, Bernhard Sprenger, Seyed Arad Moghadasi, Jakob Fleischmann, Matteo Pavan, Davide Bassani, Silvia Menin, Stefanie Rauch, Laura Krismer, Anna Sauerwein, Anne Heberle, Toni Rabensteiner, Joses Ho, Reuben S. Harris, Eduard Stefan, Rainer Schneider, Teresa Kaserer, Stefano Moro, Dorothee von Laer, Emmanuel Heilmann. A comprehensive study of SARS-CoV-2 main protease (Mpro) inhibitor-resistant mutants selected in a VSV-based system. Preprint. bioRxiv. 2023;2023.09.22.558628. Published 2023 Oct 4. https://doi.org/10.1101/2023.09.22.558628

12. Joann Chongsaritsinsuk, Alexandra D. Steigmeyer, Keira E. Mahoney, Mia A. Rosenfeld, Taryn M. Lucas, Courtney M. Smith, Alice Li, Deniz Ince, Fiona L. Kearns, Alexandria S. Battison, Marie A. Hollenhorst, D. Judy Shon, Katherine H. Tiemeyer, Victor Attah, Catherine Kwon, Carolyn R. Bertozzi, Michael J. Ferracane, Mark A. Lemmon, Rommie E. Amaro, Stacy A. Malaker. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nat Commun 14, 6169 (2023). https://doi.org/10.1038/s41467-023-41756-y

11. Ravikumar Jimmidi, Srinivas Chamakuri, Shuo Lu, Melek Nihan Ucisik, Peng-Jen Chen, Kurt M. Bohren, Seyed Arad Moghadasi, Leroy Versteeg, Christina Nnabuife, Jian-Yuan Li, Xuan Qin, Ying-Chu Chen, John C. Faver, Pranavanand Nyshadham, Kiran L. Sharma, Banumathi Sankaran, Allison Judge, Zhifeng Yu, Feng Li, Jeroen Pollet, Reuben S. Harris, Martin M. Matzuk, Timothy Palzkill, Damian W. Young. DNA-encoded chemical libraries yield non-covalent and non-peptidic SARS-CoV-2 main protease inhibitors. Communications Chemistry 6, 164 (2023). https://doi.org/10.1038/s42004-023-00961-y

10. Sang Hoon Kim, Fiona L. Kearns, Mia A. Rosenfeld, Lane Votapka, Lorenzo Casalino, Micah Papanikolas, Rommie E. Amaro, Ronit Freeman. (2023). SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx. Cell reports. Physical science4(4), 101346. https://doi.org/10.1016/j.xcrp.2023.101346

9. Seyed Arad Moghadasi, Emmanuel Heilmann, Ahmed Magdy Khalil, Christina Nnabuife, Fiona L. Kearns, Chengjin Ye, Sofia N. Moraes, Francesco Costacurta, Morgan A. Esler, Hideki Aihara, Dorothee von Laer, Luis Martinez-Sobrido, Timothy Palzkill, Rommie E. Amaro, Reuben S. Harris (2022). Transmissible SARS-CoV-2 variants with resistance to clinical protease inhibitorsScience Advances, 2023-03-31. https://doi.org/10.1101/2022.08.07.503099

8. Seyed Arad Moghadasi, Rayhan G. Biswas, Daniel A. Harki, Reuben S. Harris, Rapid resistance profiling of SARS-CoV-2 protease inhibitors, bioRxiv: the preprint server for biology doi: https://doi.org/10.1101/2023.02.25.530000

7. Emery Smith, Meredith E. Davis-Gardner, Ruben D. Garcia-Ordonez, Tu-Trinh Nguyen, Mitchell Hull, Emily Chen, Xuerong Yu, Thomas Bannister, Pierre Baillargeon, Louis Scampavia, Patrick Griffin, Michael Farzan, Timothy P. Spicer. High throughput screening for drugs that inhibit 3C-like protease in SARS-CoV-2. SLAS Discov. 2023 Apr;28(3):95-101. doi: https://doi.org/10.1016/j.slasd.2023.01.001 Epub 2023 Jan 14. PMID: 36646172; PMCID: PMC9839384. 

6. Kaïn van den Elsen, Bing Liang Alvin Chew, Jun Sheng Ho, Dahai Luo, Flavivirus nonstructural proteins and replication complexes as antiviral drug targetsCurrent Opinion in Virology, Volume 59, 2023, 101305, https://doi.org/10.1016/j.coviro.2023.101305.

5. Emmanuel Heilmann, Francesco Costacurta, Seyed Arad Moghadasi, Chengjin Ye, Matteo Pavan, Davide Bassani, Andre Volland, Claudia Ascher, Alexander Kurt Hermann Weiss, David Bante, Reuben S. Harris, Stefano Moro, Bernhard Rupp, Luis Martinez-Sobrido, Dorothee von Laer (2023). SARS-CoV-2 3CLpro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376. Science translational medicine15(678), eabq7360. https://doi.org/10.1126/scitranslmed.abq7360

4. Hannah Murphy, Hinh Ly. (2022). Understanding Immune Responses to Lassa Virus Infection and to Its Candidate Vaccines. Vaccines10(10), 1668. https://doi.org/10.3390/vaccines10101668

3. Nicholas H. Moeller, Kellan T. Passow, Daniel A. Harki, Hideki Aihara (2022). SARS-CoV-2 nsp14 Exoribonuclease Removes the Natural Antiviral 3'-Deoxy-3', 4'-dihydro-cytidine Nucleotide from RNA. Viruses14(8), 1790. https://doi.org/10.3390/v14081790

2. Fiona L. Kearns, Daniel R. Sandoval, Lorenzo Casalino, Thomas M. Clausen, Mia A. Rosenfeld, Charlotte B. Spliid, Rommie E. Amaro, Jeffrey D. Esko. (2022). Spike-heparan sulfate interactions in SARS-CoV-2 infection. Current opinion in structural biology76, 102439. https://doi.org/10.1016/j.sbi.2022.102439

1. Yang Yang, Lanying Du. (2022). Neutralizing antibodies and their cocktails against SARS-CoV-2 Omicron and other circulating variants. Cellular & molecular immunology19(8), 962–964. https://doi.org/10.1038/s41423-022-00890-1