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Gilleran, J. A., Ashraf, K., Delvillar, M., Eck, T., Fondekar, R., Miller, E. B., Hutchinson, A., Dong, A., Seitova, A., De Souza, M. Laureano, Augeri, D., Halabelian, L., Siekierka, J., Rotella, D. P., Gordon, J., Childers, W. E., Grier, M. C., Staker, B. L., Roberge, J. Y., and Bhanot, P. (2024) Structure-Activity Relationship of a Pyrrole Based Series of PfPKG Inhibitors as Anti-Malarials. J Med Chem. 67, 3467-3503
Mann, M. K., Zepeda-Velázquez, C. A., González-Álvarez, H., Dong, A., Kiyota, T., Aman, A. M., Loppnau, P., Li, Y., Wilson, B., Arrowsmith, C. H., Al-awar, R., Harding, R. J., and Schapira, M. (2021) Structure-Activity Relationship of USP5 Inhibitors. J Med Chem. 64, 15017-15036
Xiong, Y., Li, F., Babault, N., Wu, H., Dong, A., Zeng, H., Chen, X., Arrowsmith, C. H., Brown, P. J., Liu, J., Vedadi, M., and Jin, J. (2017) Structure-activity relationship studies of G9a-like protein (GLP) inhibitors. Bioorg Med Chem. 25, 4414-4423
Manz, T. D., Sivakumaren, S. C., Yasgar, A., Hall, M. D., Davis, M. I., Seo, H. - S., Card, J. D., Ficarro, S. B., Shim, H., Marto, J. A., Dhe-Paganon, S., Sasaki, A. T., Boxer, M. B., Simeonov, A., Cantley, L. C., Shen, M., Zhang, T., Ferguson, F. M., and Gray, N. S. (2020) Structure-Activity Relationship Study of Covalent Pan-phosphatidylinositol 5-Phosphate 4-Kinase Inhibitors. ACS Med Chem Lett. 11, 346-352
Bogner, A. N., and Tanner, J. J. (2022) Structure-affinity relationships of reversible proline analog inhibitors targeting proline dehydrogenase. Org Biomol Chem. 10.1039/d1ob02328d
Sanghai, Z. Assur, Liu, Q., Clarke, O. B., Belcher-Dufrisne, M., Wiriyasermkul, P., M Giese, H., Leal-Pinto, E., Kloss, B., Tabuso, S., Love, J., Punta, M., Banerjee, S., Rajashankar, K. R., Rost, B., Logothetis, D., Quick, M., Hendrickson, W. A., and Mancia, F. (2018) Structure-based analysis of CysZ-mediated cellular uptake of sulfate. Elife. 10.7554/eLife.27829
Kucera, K., A Koblansky, A., Saunders, L. P., Frederick, K. B., De La Cruz, E. M., Ghosh, S., and Modis, Y. (2010) Structure-based analysis of Toxoplasma gondii profilin: a parasite-specific motif is required for recognition by Toll-like receptor 11. J Mol Biol. 403, 616-29
D'Antonio, E. L., Deinema, M. S., Kearns, S. P., Frey, T. A., Tanghe, S., Perry, K., Roy, T. A., Gracz, H. S., Rodriguez, A., and D'Antonio, J. (2015) Structure-based approach to the identification of a novel group of selective glucosamine analogue inhibitors of Trypanosoma cruzi glucokinase. Mol Biochem Parasitol. 204, 64-76
Sheng, G., Zhao, H., Wang, J., Rao, Y., Tian, W., Swarts, D. C., van der Oost, J., Patel, D. J., and Wang, Y. (2014) Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A. 111, 652-7
Rudolph, M. J., Dutta, A., Tsymbal, A. M., McLaughlin, J. E., Chen, Y., Davis, S. A., Theodorous, S. A., Pierce, M., Algava, B., Zhang, X., Szekely, Z., Roberge, J. Y., Li, X. - P., and Tumer, N. E. (2024) Structure-based design and optimization of a new class of small molecule inhibitors targeting the P-stalk binding pocket of ricin. Bioorg Med Chem. 100, 117614
Lalonde, J. M., Le-Khac, M., Jones, D. M., Courter, J. R., Park, J., Schön, A., Princiotto, A. M., Wu, X., Mascola, J. R., Freire, E., Sodroski, J., Madani, N., Hendrickson, W. A., and Smith, A. B. (2013) Structure-Based Design and Synthesis of an HIV-1 Entry Inhibitor Exploiting X-Ray and Thermodynamic Characterization. ACS Med Chem Lett. 4, 338-343
Choi, J. Yong, Fuerst, R., Knapinska, A. M., Taylor, A. B., Smith, L., Cao, X., P Hart, J., Fields, G. B., and Roush, W. R. (2017) Structure-Based Design and Synthesis of Potent and Selective Matrix Metalloproteinase 13 Inhibitors. J Med Chem. 60, 5816-5825
Cui, H., Divakaran, A., Hoell, Z. J., Ellingson, M. O., Scholtz, C. R., Zahid, H., Johnson, J. A., Griffith, E. C., Gee, C. T., Lee, A. L., Khanal, S., Shi, K., Aihara, H., Shah, V. H., Lee, R. E., Harki, D. A., and Pomerantz, W. C. K. (2022) A Structure-based Design Approach for Generating High Affinity BRD4 D1-Selective Chemical Probes. J Med Chem. 10.1021/acs.jmedchem.1c01779
Lanier, M., Pickens, J., Bigi, S. V., Bradshaw-Pierce, E. L., Chambers, A., Cheruvallath, Z. S., Cole, D., Dougan, D. R., Ermolieff, J., Gibson, T., Halkowycz, P., Hirokawa, A., Ivetac, A., Miura, J., Nunez, E., Sabat, M., Tyhonas, J., Wang, H., Wang, X., and Swann, S. (2017) Structure-Based Design of ASK1 Inhibitors as Potential Agents for Heart Failure. ACS Med Chem Lett. 8, 316-320
Abskharon, R., Pan, H., Sawaya, M. R., Seidler, P. M., Olivares, E. J., Chen, Y., Murray, K. A., Zhang, J., Lantz, C., Bentzel, M., Boyer, D. R., Cascio, D., Nguyen, B. A., Hou, K., Cheng, X., Pardon, E., Williams, C. K., Nana, A. L., Vinters, H. V., Spina, S., Grinberg, L. T., Seeley, W. W., Steyaert, J., Glabe, C. G., Loo, R. R. Ogorzale, Loo, J. A., and Eisenberg, D. S. (2023) Structure-based design of nanobodies that inhibit seeding of Alzheimer's patient-extracted tau fibrils. Proc Natl Acad Sci U S A. 120, e2300258120
Sievers, S. A., Karanicolas, J., Chang, H. W., Zhao, A., Jiang, L., Zirafi, O., Stevens, J. T., Münch, J., Baker, D., and Eisenberg, D. (2011) Structure-based design of non-natural amino-acid inhibitors of amyloid fibril formation. Nature. 475, 96-100
Hu, D. X., Patel, S., Chen, H., Wang, S., Staben, S. T., Dimitrova, Y. N., Wallweber, H. Ackerly, Lee, J. Y., Chan, G. Ka Yan, Sneeringer, C. J., Prangley, M. S., Moffat, J. G., Wu, K. C., Schutt, L. K., Salphati, L., Pang, J., McNamara, E., Huang, H., Chen, Y., Wang, Y., Zhao, W., Lim, J., Murthy, A., and Siu, M. (2021) Structure-Based Design of Potent, Selective, and Orally Bioavailable VPS34 Kinase Inhibitors. J Med Chem. 10.1021/acs.jmedchem.1c01180
Seo, M., Kim, J. - D., Neau, D., Sehgal, I., and Lee, Y. - H. (2011) Structure-based development of small molecule PFKFB3 inhibitors: a framework for potential cancer therapeutic agents targeting the Warburg effect. PLoS One. 6, e24179
Bogner, A. N., Ji, J., and Tanner, J. J. (2022) Structure-based engineering of minimal Proline dehydrogenase domains for inhibitor discovery. Protein Eng Des Sel. 10.1093/protein/gzac016
Martin, S. E. S., Tan, Z. - W., Itkonen, H. M., Duveau, D. Y., Paulo, J. A., Janetzko, J., Boutz, P. L., Törk, L., Moss, F. A., Thomas, C. J., Gygi, S. P., Lazarus, M. B., and Walker, S. (2018) Structure-Based Evolution of Low Nanomolar O-GlcNAc Transferase Inhibitors. J Am Chem Soc. 10.1021/jacs.8b07328
Seidler, P. Matthew, Boyer, D. R., Murray, K. A., Yang, T. P., Bentzel, M., Sawaya, M. R., Rosenberg, G., Cascio, D., Williams, C. Kazu, Newell, K. L., Ghetti, B., DeTure, M. A., Dickson, D. W., Vinters, H. V., and Eisenberg, D. S. (2019) Structure-based inhibitors halt prion-like seeding by Alzheimer's disease-and tauopathy-derived brain tissue samples. J Biol Chem. 294, 16451-16464
Zuo, Y., and Steitz, T. A. (2017) A structure-based kinetic model of transcription. Transcription. 8, 1-8
Song, J., Teplova, M., Ishibe-Murakami, S., and Patel, D. J. (2012) Structure-based mechanistic insights into DNMT1-mediated maintenance DNA methylation. Science. 335, 709-12
Gorelik, M., Manczyk, N., Pavlenco, A., Kurinov, I., Sidhu, S. S., and Sicheri, F. (2018) A Structure-Based Strategy for Engineering Selective Ubiquitin Variant Inhibitors of Skp1-Cul1-F-Box Ubiquitin Ligases. Structure. 10.1016/j.str.2018.06.004
Sheng, G., Gogakos, T., Wang, J., Zhao, H., Serganov, A., Juranek, S., Tuschl, T., Patel, D. J., and Wang, Y. (2017) Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes. Nucleic Acids Res. 45, 9149-9163

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