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9. Gang Ye, Fan Bu, Hailey Turner-Hubbard, Morgan Herbst, Lanying Du, Ge Yang, Bin Liu, Fang Li. Structures of Marburgvirus glycoprotein and its complex with NPC1 receptor. Nature. 2026 May;653(8114):621-626. PMID: 41813895 PMCID: PMC13171430 DOI: 10.1038/s41586-026-10240-0
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7. Fan Bu, Gang Ye, Kimberly Morsheimer, Hailey Turner-Hubbard, Brett Eaton, Manu Anantpadma, Khaggeswar Bheemanapally, Chalet Tan, Robert Davey, Fang Li A highly potent and broadly accessible bispecific nanobody for the treatment of ebola virus infections. PLoS Pathog. 2026 Jan 27;22(1):e1013878. PMID: 41592114 PMCID: PMC12858065 DOI: 10.1371/journal.ppat.1013878
6. Alma C Castañeda-Leautaud, Ambuj Srivastava, Eunjung Kim, Donghoon Chung, Thomas D Bannister, Rommie E Amaro. Discovery of Tetrahydroisoquinoline-Based SARS-CoV-2 Helicase Inhibitors with Iterative, Deep Learning-Enhanced Virtual Screening. J Chem Inf Model. 2026 Jan 12;66(1):541-553. PMID: 41400222 DOI: 10.1021/acs.jcim.5c02059
5. Huihui Mou, Bo Gao, Gang Ye, Lizhou Zhang, Divyasha Saxena, Fan Bu, Jyoti Vishwakarma, Shuo Zhou, Claudia Ruiz Bayona, Li Lin, Yulia Getmanenko, Janarjan Bhandari, Charles C Bailey, Gogce C Crynen, Claire E Kitzmiller, Hao Li, Yuka Otsuka, Chao Wang, Lalit Batra, Stuart Weston, Matthew B Frieman, David K Meyerholz, Louis Scampavia, Timothy P Spicer, Reuben S Harris, Michael D Cameron, Thomas D Bannister, Jian Zheng, Michael Farzan, Fang Li, Hyeryun Choe. A SARS-CoV-2 entry inhibitor trimerizes to lock the spike protein in a closed conformation. bioRxiv [Preprint]. 2025 Nov 19:2025.11.19.689107. PMID: 41982337 PMCID: PMC13073230 DOI: 10.1101/2025.11.19.689107
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3. Donghoon Chung, Yuka Otsuka, Eunjung Kim, Sultan Ullah, Nicole M. Kennedy, Khac Huy Ngo, Jinjoo Kang, Reece Tomlinson, Brian Alejandro, Koji Barnaby, Jeffrey Miller, Justin Shumate, Chwee Fang Teo, Yaw Bia Tan, Che Shin Chew, CongBao Kang, Dahai Luo, Louis Scampavia, Timothy P. Spicer, Thomas D. Bannister. (2026) “Discovery of a potent anti-Zika virus benzamide series targeting the viral protein NS4B.” PLoS Pathog 22(4): e1013609. PMID: 41931535 PMCID: PMC13065080 DOI: 10.1371/journal.ppat.1013609
2. Kristin V. Lyles, Shannon Stone, Priti Singh, Lila D. Patterson, Janhavi Natekar, Heather Pathak, Rohit K. Varshnaya, Amany Elsharkawy, Dongning Liu, Shubham Bansal, Oluwafoyinsola O. Faniyi, Sijia Tang, Xiaoxiao Yang, Nagaraju Mulpuri, Donald Hamelberg, Congbao Kang, Binghe Wang, Mukesh Kumar, Ming Luo. 2025. "Entry Inhibitors of SARS-CoV-2 Targeting the Transmembrane Domain of the Spike Protein" Viruses 17, no. 7: 989. PMID: 40733606 PMCID: PMC12300635 DOI: 10.3390/v17070989
1. 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. J Phys Chem B. 2026 Jan 15;130(2):730-740. DOI: 10.1021/acs.jpcb.5c08598 PMID: 37645037 PMCID: PMC10462179
2025
9. Flury P, Vishwakarma J, Sylvester K, Higashi-Kuwata N, Dabrowska AK, Delgado R, Cuell A, Basu R, Taylor AB, de Oliveira EG, Magalhães Serafim MS, Qiao J, Chen Y, Yang S, O'Donoghue AJ, Mitsuya H, Gütschow M, Laufer SA, Müller CE, Harris RS, Pillaiyar T. Azapeptide-Based SARS-CoV-2 Main Protease Inhibitors: Design, Synthesis, Enzyme Inhibition, Structural Determination, and Antiviral Activity. J Med Chem. 2025 Sep 25;68(18):19339-19376 PMID: 40932417 PMCID: PMC12481482 DOI: 10.1021/acs.jmedchem.5c01520
8. Kunyang Sun, Dorian Bagni, Joseph M Cavanagh, Yingze Wang, Jacob M Sawyer, Bo Zhou, Andrew Gritsevskiy, Oufan Zhang, Teresa Head-Gordon. SynLlama: Generating Synthesizable Molecules and Their Analogs with Large Language Models (2025). ACS Cent Sci 2025 Vol. 11 Issue 11 Pages 2108-2120 Accession Number: 41341056 PMCID: PMC12670306 DOI: 10.1021/acscentsci.5c01285
7. Vaskuri GJ, Ye G, Bu F, Yang D, Jonsson CB, Turner-Hubbard H, Winecke S, Mendoza A, Li F, Tan C. Long-Circulating Nanobody Confers Durable Prophylaxis against Severe Acute Respiratory Syndrome Coronavirus 2 Omicron Infection. Adv Nanobiomed Res. 2025 Aug;5(8). DOI: 10.1002/anbr.202400214. Epub 2025 Jun 27. PubMed PMID: 40851835; PubMed Central PMCID: PMC12369981.
6. Morgan A Esler, Ke Shi, Joseph A Rollie, Renee Delgado, Jyoti Vishwakarma, Agnieszka Dabrowska, Janani Prahlad, Seyed Arad Moghadasi, Reuben S Harris, Hideki Aihara. Structural basis for varying drug resistance of SARS-CoV-2 Mpro E166 variants. mBio. 2025 Jul 9;16(7):e0262424. doi: 10.1128/mbio.02624-24. Epub 2025 Jun 2. PMID: 40454888; PMCID: PMC12239574.
5. Anurag Misra, R Rahisuddin, Manish Parihar, Shailee Arya, Thiruselvam Viswanathan, Nathaniel Jackson, Shan Qi, Siu-Hong Chan, Reuben S Harris, Luis Martinez-Sobrido, Yogesh K Gupta. Structural insights into the assembly and regulation of 2'-O RNA methylation by SARS-CoV-2 nsp16/nsp10. Structure. 2025 Jun 5;33(6):1027-1039.e4. doi: 10.1016/j.str.2025.03.009. Epub 2025 Apr 11. PMID: 40220753; PMCID: PMC12145257.
4. Yingze Wang, Kunyang Sun, Jie Li, Xingyi Guan, Oufan Zhang, Dorian Bagni, Yang Zhang, Heather A Carlson, Teresa Head-Gordon. A workflow to create a high-quality protein-ligand binding dataset for training, validation, and prediction tasks. Digit Discov. 2025 Apr 2;4(5):1209-1220. doi: 10.1039/d4dd00357h. PMID: 40190768; PMCID: PMC11967698
3. 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. 2024 Dec 23;20(12):e1012817. doi: 10.1371/journal.ppat.1012817. PMID: 39715280; PMCID: PMC11723632.
2. 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 PubMed PMID: 39680623; PMCID: PMC12381577.
1. 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. 2025 Feb 2;8(1):156. doi: 10.1038/s42003-025-07613-y. PMID: 39894818; PMCID: PMC11788421.
2024
13. 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 Dec 23;64(24):9082-9097. doi: 10.1021/acs.jcim.4c00634. Epub 2024 Jun 6. PMID: 38843070; PMCID: PMC11683870.
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11. 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. 2024 Nov 26;20(11):e1012726. doi: 10.1371/journal.ppat.1012726. PMID: 39591462; PMCID: PMC11630572.
10. 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. 2024 Sep 26;20(9):e1012600. doi: 10.1371/journal.ppat.1012600. PMID: 39325826; PMCID: PMC11460708.
9. 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. PLoS Pathog. 2024 Sep 11;20(9):e1012522. doi: 10.1371/journal.ppat.1012522. PMID: 39259728; PMCID: PMC11407635.
8. 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. 2024 Sep 5;20(9):e1012493. doi: 10.1371/journal.ppat.1012493. PMID: 39236072; PMCID: PMC11407660.
7. 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 & D, 2024 Sep;29(6):100180. doi: 10.1016/j.slasd.2024.100180. Epub 2024 Aug 22. PMID: 39173831. PMCID: PMC12377702.
6. Yuka Otsuka, Lizhou Zhang, Huihui Mou, Justin Shumate, Claire E Kitzmiller, Louis Scampavia, Thomas D Bannister, Michael Farzan, Hyeryun Choe, Timothy P Spicer. Simultaneous screening for selective SARS-CoV-2, Lassa, and Machupo virus entry inhibitors. SLAS discovery : advancing life sciences R & D, 2024 Sep;29(6):100178. doi: 10.1016/j.slasd.2024.100178.100178. Epub 2024 Aug 17. PMID: 39159824; PMCID: PMC11542554.
5. 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. SARS-CoV-2 Mpro inhibitor identification using a cellular gain-of-signal assay for high-throughput screening. SLAS discovery : advancing life sciences R & D, 2024 Sep;29(6):100181. doi: 10.1016/j.slasd.2024.100181. Epub 2024 Aug 22. PMID: 39173830; PMCID: PMC11550483.
4. Yang Yang, Fang Li, Lanying Du. Therapeutic nanobodies against SARS-CoV-2 and other pathogenic human coronaviruses. J Nanobiotechnology. 2024 May 31;22(1):304. doi: 10.1186/s12951-024-02573-7. PMID: 38822339; PMCID: PMC11140877.
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1. Juan Shi, Jian Zheng, Xiujuan Zhang, Wanbo Tai, Ryan Compas, Jack Deno, Natalie Jachym, Abhishek K Verma, Gang Wang, Xiaoqing Guan, Abby E Odle, Yushun Wan, Fang Li, Stanley Perlman, Liang Qiao, Lanying Du. A T cell-based SARS-CoV-2 spike protein vaccine provides protection without antibodies. JCI Insight. 2024 Mar 8;9(5):e155789. PMID: 38456504 PMCID: PMC10972590 DOI: 10.1172/jci.insight.155789
2023
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1. 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. SARS-CoV-2 3CLpro mutations selected in a VSV-based system confer resistance to nirmatrelvir, ensitrelvir, and GC376. Science translational medicine, 2023 Jan 11;15(678):eabq7360. doi: 10.1126/scitranslmed.abq7360. Epub 2023 Jan 11. PMID: 36194133; PMCID: PMC9765458.
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3. Nicholas H. Moeller, Kellan T. Passow, Daniel A. Harki, Hideki Aihara. SARS-CoV-2 nsp14 Exoribonuclease Removes the Natural Antiviral 3'-Deoxy-3', 4'-dihydro-cytidine Nucleotide from RNA. Viruses, 2022 Aug 16;14(8):1790. doi: 10.3390/v14081790. PMID: 36016411; PMCID: PMC9415739.
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