Scientific publications empower scientists worldwide to build upon existing knowledge and drive scientific progress.
READDI-AC discoveries, supported by NIH award U1AI171292, are shared with the broader community through scientific publications, which can be found below:
Manuscripts in Press
| Title | Authors | Journal |
|---|---|---|
| Allosteric Binders of ACE2 Are Promising Anti-SARS-CoV-2 Agents | Hochuli, Joshua E; Jain, Sankalp; Melo-Filho, Cleber; Sessions, Zoe L; Bobrowski, Tesia; Choe, Jun; Zheng, Johnny; Eastman, Richard; Talley, Daniel C; Rai, Ganesha; Simeonov, Anton; Tropsha, Alexander; Muratov, Eugene N; Baljinnyam, Bolormaa; Zakharov, Alexey V | ACS Pharmacology & Translational Science |
| Conserved coronavirus proteins as targets of broad-spectrum antivirals. | Melo-Filho, Cleber C; Bobrowski, Tesia; Martin, Holli-Joi; Sessions, Zoe; Popov, Konstantin I; Moorman, Nathaniel J; Baric, Ralph S; Muratov, Eugene N; Tropsha, Alexander | Antiviral Research |
| Discovery of New Zika Protease and Polymerase Inhibitors through the Open Science Collaboration Project OpenZika | Mottin, Melina; de Paula Sousa, Bruna Katiele; de Moraes Roso Mesquita, Nathalya Cristina; de Oliveira, Ketllyn Irene Zagato; Noske, Gabriela Dias; Sartori, Geraldo Rodrigues; de Oliveira Albuquerque, Aline; Urbina, Fabio; Puhl, Ana C; Moreira-Filho, José Teófilo; Souza, Guilherme E; Guido, Rafael V C; Muratov, Eugene; Neves, Bruno Junior; Martins da Silva, João Hermínio; Clark, Alex E; Siqueira-Neto, Jair L; Perryman, Alexander L; Oliva, Glaucius; Ekins, Sean; Andrade, Carolina Horta | Journal of Chemical Information and Modeling |
| SARS-CoV-2 infection produces chronic pulmonary epithelial and immune cell dysfunction with fibrosis in mice. | Dinnon 3rd, Kenneth H; Leist, Sarah R; Okuda, Kenichi; Dang, Hong; Fritch, Ethan J; Gully, Kendra L; De la Cruz, Gabriela; Evangelista, Mia D; Asakura, Takanori; Gilmore, Rodney C; Hawkins, Padraig; Nakano, Satoko; West, Ande; Schäfer, Alexandra; Gralinski, Lisa E; Everman, Jamie L; Sajuthi, Satria P; Zweigart, Mark R; Dong, Stephanie; McBride, Jennifer; Cooley, Michelle R; Hines, Jesse B; Love, Miriya K; Groshong, Steve D; VanSchoiack, Alison; Phelan, Stefan J; Liang, Yan; Hether, Tyler; Leon, Michael; Zumwalt, Ross E; Barton, Lisa M; Duval, Eric J; Mukhopadhyay, Sanjay; Stroberg, Edana; Borczuk, Alain; Thorne, Leigh B; Sakthivel, Muthu K; Lee, Yueh Z; Hagood, James S; Mock, Jason R; Seibold, Max A; O'Neal, Wanda K; Montgomery, Stephanie A; Boucher, Richard C; Baric, Ralph S | Science Translational Medicine |
| Small Molecule Antiviral Compound Collection (SMACC): a database to support the discovery of broad-spectrum antiviral drug molecules. | Martin, Holli-Joi; Melo-Filho, Cleber C; Korn, Daniel; Eastman, Richard T; Rai, Ganesha; Simeonov, Anton; Zakharov, Alexey V; Muratov, Eugene; Tropsha, Alexander | Antiviral Research |
| A low-background, fluorescent assay to evaluate inhibitors of diverse viral proteases. | Leonard, Rebecca A; Rao, Vishwas N; Bartlett, Alexandria; Froggatt, Heather M; Luftig, Micah A; Heaton, Brook E; Heaton, Nicholas S | Journal of Virology |
| A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus. | Tse, Longping V; Hou, Yixuan J; McFadden, Elizabeth; Lee, Rhianna E; Scobey, Trevor D; Leist, Sarah R; Martinez, David R; Meganck, Rita M; Schäfer, Alexandra; Yount, Boyd L; Mascenik, Teresa; Powers, John M; Randell, Scott H; Zhang, Yi; Wang, Lingshu; Mascola, John; McLellan, Jason S; Baric, Ralph S | Science Translational Medicine |
| Clinical and Translational Pharmacology Considerations for Anti-infectives Approved Under the FDA Animal Rule. | Temrikar, Zaid H; Golden, Jennifer E; Jonsson, Colleen B; Meibohm, Bernd | Clinical Pharmacokinetics |
| Efficacy of the oral nucleoside prodrug GS-5245 (Obeldesivir) against SARS-CoV-2 and coronaviruses with pandemic potential. | Martinez, David R; Moreira, Fernando R; Zweigart, Mark R; Gully, Kendra L; De la Cruz, Gabriela; Brown, Ariane J; Adams, Lily E; Catanzaro, Nicholas; Yount, Boyd; Baric, Thomas J; Mallory, Michael L; Conrad, Helen; May, Samantha R; Dong, Stephanie; Scobey, D Trevor; Montgomery, Stephanie A; Perry, Jason; Babusis, Darius; Barrett, Kimberly T; Nguyen, Anh-Hoa; Nguyen, Anh-Quan; Kalla, Rao; Bannister, Roy; Bilello, John P; Feng, Joy Y; Cihlar, Tomas; Baric, Ralph S; Mackman, Richard L; Schäfer, Alexandra; Sheahan, Timothy P | Science Translational Medicine |
| Host range, transmissibility and antigenicity of a pangolin coronavirus. | Hou, Yixuan J; Chiba, Shiho; Leist, Sarah R; Meganck, Rita M; Martinez, David R; Schäfer, Alexandra; Catanzaro, Nicholas J; Sontake, Vishwaraj; West, Ande; Edwards, Catlin E; Yount, Boyd; Lee, Rhianna E; Gallant, Samuel C; Zost, Seth J; Powers, John; Adams, Lily; Kong, Edgar F; Mattocks, Melissa; Tata, Aleksandra; Randell, Scott H; Tata, Purushothama R; Halfmann, Peter; Crowe Jr, James E; Kawaoka, Yoshihiro; Baric, Ralph S | Nature Microbiology |
| Lies and Liabilities: Computational Assessment of High-Throughput Screening Hits to Identify Artifact Compounds | Alves, Vinicius M; Yasgar, Adam; Wellnitz, James; Rai, Ganesha; Rath, Marielle; Braga, Rodolpho C; Capuzzi, Stephen J; Simeonov, Anton; Muratov, Eugene N; Zakharov, Alexey V; Tropsha, Alexander | Journal of Medicinal Chemistry |
| Praemonitus praemunitus: can we forecast and prepare for future viral disease outbreaks? | Sessions, Zoe; Bobrowski, Tesia; Martin, Holli-Joi; Beasley, Jon-Michael T; Kothari, Aneri; Phares, Trevor; Li, Michael; Alves, Vinicius M; Scotti, Marcus T; Moorman, Nathaniel J; Baric, Ralph; Tropsha, Alexander; Muratov, Eugene N | FEMS Microbiology Reviews |
| A nano-luciferase expressing human coronavirus OC43 for countermeasure development. | Diefenbacher, Meghan V; Baric, Thomas J; Martinez, David R; Baric, Ralph S; Catanzaro, Nicholas J; Sheahan, Timothy P | Virus Research |
| An oral non-covalent non-peptidic inhibitor of SARS-CoV-2 Mpro ameliorates viral replication and pathogenesis in vivo | Nian E. Zhou, Su Tang, Xuelin Bian, Maloy K. Parai, Inna V. Krieger, Armando Flores, Pradeep K. Jaiswal, Radha Bam, Jeremy L. Wood, Zhe Shi1, Laura J. Stevens, Trevor Scobey, Meghan V. Diefenbacher, Fernando R. Moreira, Thomas J. Baric, Arjun Acharya, Joonyoung Shin, Manish M. Rathi, Karen C. Wolff, Laura Riva, Malina A. Bakowski, Case W. McNamara, Nicholas J. Catanzaro, Rachel L. Graham, David C. Schultz, Sara Cherry, Yoshihiro Kawaoka, Peter J. Halfmann, Ralph S. Baric, Mark R. Denison, Timothy P. Sheahan*, James C. Sacchettini*.Co-crresponding* | Cell Reports |
| Dihydropyrazolo[1,5-a]pyrazin-4(5H)-ones as Cyclic Products of β-Amidomethyl Vinyl Sulfone Alphavirus Cysteine Protease Inhibitors. | Ghoshal A, Magalhães ÁF, Asressu KH, Hossain MA, Todd MH, Willson TM. | Pharmaceuticals |
| Disparate SARS-CoV-2 Infection Outcomes Abound, but What Makes SARS-CoV-2 Bound for Rebound? | Timothy P. Sheahan | Journal of Infectious Diseases |
| HIt Discovery using docking ENriched by GEnerative Modeling (HIDDEN GEM): A novel computational workflow for accelerated virtual screening of ultra-large chemical libraries. | Popov, Konstantin I; Wellnitz, James; Maxfield, Travis; Tropsha, Alexander | Molecular Informatics |
| Identification of a cell-active chikungunya virus nsP2 protease inhibitor using a covalent fragment-based screening approach | Merten, E.M., Sears, J.D., Leisner, T.M., Hardy, P.B., Ghoshal, A., Hossain, M.A., Asressu, K.H., Brown, P.J., Tse, E.G., Stashko, M.A., Li, K., Norris-Drouin, J.L., Herring, L.E., Mordant, A.L., Webb, T.S., Mills, C.A., Barker, N.K., Streblow, Z.J., Perveen, S., Arrowsmith, C.H., Couñago, R.M., Arnold, J.J., Cameron, C.E., Streblow, D.N., Moorman, N.J., Heise, M.T., Willson, T.M., Popov, K.I., and Pearce, K.H. | Proceedings of the National Academy of Sciences of the United States of America |
| Mapping of susceptibility loci for Ebola virus pathogenesis in mice. | Schäfer, Alexandra; Marzi, Andrea; Furuyama, Wakako; Catanzaro, Nicholas J; Nguyen, Cameron; Haddock, Elaine; Feldmann, Friederike; Meade-White, Kimberly; Thomas, Tina; Hubbard, Miranda L; Gully, Kendra L; Leist, Sarah R; Hock, Pablo; Bell, Timothy A; De la Cruz, Gabriela E; Midkiff, Bentley R; Martinez, David R; Shaw, Ginger D; Miller, Darla R; Vernon, Michael J; Graham, Rachel L; Cowley, Dale O; Montgomery, Stephanie A; Schughart, Klaus; de Villena, Fernando Pardo Manuel; Wilkerson, Gregory K; Ferris, Martin T; Feldmann, Heinz; Baric, Ralph S | Cell Reports |
| Mechanism and spectrum of inhibition of a 4'-cyano modified nucleotide analog against diverse RNA polymerases of prototypic respiratory RNA viruses. | Gordon, Calvin J; Walker, Simon M; Tchesnokov, Egor P; Kocincova, Dana; Pitts, Jared; Siegel, Dustin S; Perry, Jason K; Feng, Joy Y; Bilello, John P; Götte, Matthias | Journal of Biological Chemistry |
| Proximal Fleximer Analogues of 2′-deoxy-2′-fluoro-2′-methyl Purine Nucleos(t)ides: Synthesis and Preliminary Pharmacokinetic and Antiviral Evaluation. | Waters III, C. D.; Carlyle, E.; Smart, V.; Rege, A.; Bieberich, C.J.; Seley-Radtke, K. L.* | Bioorganic & Medicinal Chemistry |
| SARS-CoV-2 variant of concern fitness and adaptation in primary human airway epithelia. | Meganck, Rita M; Edwards, Caitlin E; Mallory, Michael L; Lee, Rhianna E; Dang, Hong; Bailey, Alexis B; Wykoff, Jason A; Gallant, Samuel C; Zhu, Deanna R; Yount, Boyd L; Kato, Takafumi; Shaffer, Kendall M; Nakano, Satoko; Cawley, Anne Marie; Sontake, Vishwaraj; Wang, Jeremy R; Hagan, Robert S; Miller, Melissa B; Tata, Purushothama Rao; Randell, Scott H; Tse, Longping V; Ehre, Camille; Okuda, Kenichi; Boucher, Richard C; Baric, Ralph S | Cell Reports |
| Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of Chikungunya nsP2 Cysteine Protease with Antialphavirus Activity. | Ghoshal A, Asressu KH, Hossain MA, Brown PJ, Nandakumar M, Vala A, Merten EM, Sears JD, Law I, Burdick JE, Morales NL, Perveen S, Pearce KH, Popov KI, Moorman NJ, Heise MT, Willson TM | Journal of Medicinal Chemistry |
| The antiviral, BDGR-49, provides protection from lethal, neurotropic Venezuelan Equine Encephalitis Virus intranasal infection in mice. | Evan Williams, Yi Xue, Peter Vogel, Dong Yang, Alejandro Ponce-Flores, Xiaoyu Li, Tyler Tyler Ogorek, Manisha Saini, Jorge Iulek, Francesc Ruiz, Eddy Arnold, Jennifer Golden, Bernd Meibohm, and Colleen Jonsson. | Science Translational Medicine |
| The oral nucleoside prodrug GS-5245 is efficacious against SARS-CoV-2 and other endemic, epidemic, and enzootic coronaviruses. | Martinez, David R; Moreira, Fernando R; Catanzaro, Nicholas J; Diefenbacher, Meghan V; Zweigart, Mark R; Gully, Kendra L; De la Cruz, Gabriela; Brown, Ariane J; Adams, Lily E; Yount, Boyd; Baric, Thomas J; Mallory, Michael L; Conrad, Helen; May, Samantha R; Dong, Stephanie; Scobey, D Trevor; Nguyen, Cameron; Montgomery, Stephanie A; Perry, Jason K; Babusis, Darius; Barrett, Kimberly T; Nguyen, Anh-Hoa; Nguyen, Anh-Quan; Kalla, Rao; Bannister, Roy; Feng, Joy Y; Cihlar, Tomas; Baric, Ralph S; Mackman, Richard L; Bilello, John P; Schäfer, Alexandra; Sheahan, Timothy P | Science Translational Medicine |
| The small molecule inhibitor of SARS-CoV-2 3CLpro EDP-235 prevents viral replication and transmission in vivo | Rhodin, Michael H J; Reyes, Archie C; Balakrishnan, Anand; Bisht, Nalini; Kelly, Nicole M; Gibbons, Joyce Sweeney; Lloyd, Jonathan; Vaine, Michael; Cressey, Tessa; Crepeau, Miranda; Shen, Ruichao; Manalo, Nathan; Castillo, Jonathan; Levene, Rachel E; Leonard, Daniel; Zang, Tianzhu; Jiang, Lijuan; Daniels, Kellye; Cox, Robert M; Lieber, Carolin M; Wolf, Josef D; Plemper, Richard K; Leist, Sarah R; Scobey, Trevor; Baric, Ralph S; Wang, Guoqiang; Goodwin, Bryan; Or, Yat Sun | Nature Communications |
| U-CAN-seq: A Universal Competition Assay by Nanopore Sequencing. | Diaz, Jennifer; Sears, John; Chang, Che-Kang; Burdick, Jane; Law, Isabella; Sanders, Wes; Linnertz, Colton; Sylvester, Paul; Moorman, Nathaniel; Ferris, Martin T; Heise, Mark T | Viruses |
| Dysregulation of lung epithelial cell homeostasis and immunity contributes to Middle East Respiratory Syndrome coronavirus disease severity | Amy C. Sims, Alexandra Schäfer, Kenichi Okuda, Sarah R. Leist, Jacob F. Kocher, Adam S. Cockrell, Padraig E. Hawkins, Minako Furusho, Kara L. Jensen, Jennifer E. Kyle, Kristin E. Burnum-Johnson, Kelly G. Stratton, Natalie C. Lamar, Carrie D. Niccora, Karl K. Weitz, Richard D. Smith, Thomas O. Metz, Katrina M. Waters, Richard C. Boucher, Stephanie A. Montgomery, Ralph S. Baric*, Timothy P. Sheahan*. Co-crresponding* | mSphere |
| On the importance of data curation for knowledge mining in antiviral research | Martin, Holli-Joi; Melo-Filho, Cleber C; Zakharov, Alexey V; Muratov, Eugene; Tropsha, Alexander | Science Progress |
Pre-Prints
| Title | Authors |
|---|---|
| A Covalent Chemical Probe for Chikungunya nsP2 Cysteine Protease with Antialphaviral Activity and Proteome-wide Selectivity | Ghoshal A, Tse EG, Hossain MA, Kesatebrhan, Asressu KH, Merten EM, Sears JD, Howell S, Perveen S, Burdick J, Morales NL, Martinez SA, Law I, Davenport BJ, Morrison TE, Streblow ZJ, Streblow DN, Mordant AL, Webb TS, Cabrera A, Herring LE, Arrowsmith CH, Pearce KH, Moorman NJ, Heise MT, Couñago RM, Brown PJ, Willson TM. |
| Designed miniproteins potently inhibit and protect against MERS-CoV | Ragotte, Robert J; Tortorici, M Alejandra; Catanzaro, Nicholas J; Addetia, Amin; Coventry, Brian; Froggatt, Heather M; Lee, Jimin; Stewart, Cameron; Brown, Jack T; Goreshnik, Inna; Sims, Jeremiah N; Milles, Lukas F; Wicky, Basile I M; Glögl, Matthias; Gerben, Stacey; Kang, Alex; Bera, Asim K; Sharkey, William; Schäfer, Alexandra; Baric, Ralph S; Baker, David; Veesler, David |
| Heli-SMACC: Helicase-targeting SMAll Molecule Compound Collection. | Martin, Holli-Joi; Hossain, Mohammad A; Wellnitz, James; Kelestemur, Enes; Hochuli, Joshua E; Parveen, Sumera; Arrowsmith, Cheryl; Willson, Timothy M; Muratov, Eugene; Tropsha, Alexander |
| Identification of Inhibitors of Chikungunya Virus nsP2 ATPase | Navarro H, Scott JE, Smith GR, Ghiabi P, Gibson E, Loppnau P, Harding RJ, Hossain MA, Bose MR, Pearce KH, Merten EM, Willson TM, Brown PJ |
| Identifying novel chemical matter against the Chikungunya virus nsP3 macrodomain through crystallographic fragment screening. | Aschenbrenner, Jasmin C; de Godoy, Andre Schutzer; Fairhead, Michael; Tomlinson, Charles W E; Winokan, Max; Balcomb, Blake H; Capkin, Eda; Chandran, Anu V; Golding, Mathew; Koekemoer, Lizbe; Lithgo, Ryan M; Marples, Peter G; Ni, Xiaomin; Thompson, Warren; Wild, Conor; Xavier, Mary-Ann E; Fearon, Daren; von Delft, Frank |
| A post-assembly conformational change makes the SARS-CoV-2 polymerase elongation-competent | Klein, Misha; Das, Arnab; Bera, Subhas C; Anderson, Thomas K; Kocincova, Dana; Lee, Hery W; Wang, Bing; Papini, Flavia S; Marecki, John C; Arnold, Jamie J; Cameron, Craig E; Raney, Kevin D; Artsimovitch, Irina; Götte, Mathias; Kirchdoerfer, Robert N; Depken, Martin; Dulin, David |
| Single-molecule assay reveals the impact of composition, RNA duplex, and inhibitors on the binding dynamics of SARS-CoV-2 polymerase complex | Lovell, Terri C; Dewling, Heidi A F; Li, Cynthia X; Lee, Hery W; Gordon, Calvin J; Kocincova, Dana; Badmalia, Maulik D; Tchesnokov, Egor P; Götte, Matthias; Cosa, Gonzalo |
| Species Dependent Metabolism of a Covalent nsP2 Protease Inhibitor with in Vivo Anti-alphaviral Activity | Hossain MA, Mayo AK, Ghoshal A, Taft-Benz SA, Anderson EJ, Morales NL, Pressey KD, Vargason AM, Brouwer KLR, Moorman NJ, Heise MT, Willson TM |