Publications
Challenges of Biological Complexity in the Study of Nanotoxicology
Northwick, A.B.; Carlson, E. E. Chem. Res. Toxicol. 2024
kinact/KI Value Determination for Penicillin-Binding Proteins in Live Cells
Shirley, J.D.;† Gillingham, J.R.;† Nauta, K.M.;† Diwakar, S.; Carlson, E. E. ACS Infect. Dis. 2024
† Co-first authors
Evaluation of Expanded 2-Aminobenzothiazole Library as Inhibitors of a Model Histidine Kinase and Virulence Suppressors in Pseudomonas aeruoginosa
Fihn, C. A.; Lembke, H. K.; Gaulin, J.; Bouchard, P.; Penningroth, M. R.; Crone, K. K.; Vogt, G. A.; Gilbertsen, A. J.; Ayotte, Y.; Couthino de Oliveira, L.; Serrano-Wu, M. H.; Drouin, N.; Hung, D. T.; Hunter, R. C.; Carlson, E. E. Bioorganic Chem., 2024, 153, 107840.
HUHgle: An Interactive Substrate Design Tool for Covalent Protein-ssDNA Labeling Using HUH-Tags
Smiley, A.T., Babilonia-Díaz, N.S., Hughes, A.J., Lemmex, A.C.D., Anderson, M.J.M., Tompkins, K.J., and Gordon, W.R. ACS Synthetic Biology 2024
Guiding the Way: Traditional Medicinal Chemistry Inspiration for Rational Gram-Negative Drug Design
Stoorza, A.M. and Duerfeldt, A.S. Journal of Medicinal Chemistry 2024 67 (1), 65-80
Penicillin-binding protein redundancy in Bacillus subtilis enables growth during alkaline shock
Mitchell, S. M., Kearns, D. B. and Carlson, E. E. Appl. Environ. Microbiol., 2024, 90, e0054823.
Development of allosteric and selective CDK2 inhibitors of contraception with negative cooperativity to cyclin binding
Faber, E.B., Sun, L., Tang, J., Roberts, E., Ganeshkumar, S., Wang, N., Rasmussen, D., Majumdar, A., Hirsch, L.E., John, K., Yang, A., Khalid, H., Hawkinson, J.E., Levinson, N.M., Chennathukuzhi, V., Harki, D.A., Schönbrunn , E., Georg, G.I., Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding. Nat Commun 14, 3213 (2023).
https://doi.org/10.1038/s41467-023-38732-x
Development of Allosteric NIK Ligands from Fragment-Based NMR Screening
Jared J. Anderson, Michael J. Grillo, and Daniel A. Harki
ACS Medicinal Chemistry Letters 2023 14 (12), 1815-1820
https://doi.org/10.1021/acsmedchemlett.3c00429
Synthesis, Enzymatic Peptide Incorporation, and Applications of Diazirine-Containing Isoprenoid Diphosphate Analogues
Katarzyna Justyna, Riki Das, Ellen L. Lorimer, Jiayue Hu, Jodi S. Pedersen, Andrea M. Sprague-Getsy, Garrett L. Schey, Michelle A. Sieburg, Olivia J. Koehn, Yen-Chih Wang, Yong-Xiang Chen, James L. Hougland, Carol L. Williams, and Mark D. Distefano
Organic Letters 2023 25 (36), 6767-6772
https://doi.org/10.1021/acs.orglett.3c02736
Understanding ATP Binding to DosS Catalytic Domain with a short ATP-Lid
Grant W. Larson, Peter K. Windsor, Elizabeth Smithwick, Ke Shi, Hideki Aihara, Anoop Rama Damodaran, and Ambika Bhagi-Damodaran
Biochemistry 2023 62 (22), 3283-3292
GTPase splice variants RAC1 and RAC1B display isoform-specific differences in localization, prenylation, and interaction with the chaperone protein SmgGDS
Koehn, O. J.; Lorimer, E.; Unger, B.; Harris, R. M.; Das, A. S.; Suazo, K. F.; Auger, S. A.; Distefano, M. D.; Prokop, J. W.; Williams, C. L. GTPase splice variants RAC1 and RAC1B display isoform-specific differences in localization, prenylation, and interaction with the chaperone protein SmgGDS. J. Biol. Chem., 2023, 299, 104698.
Modern Materials Provoke Ancient Behavior: Bacterial Resistance to Metal Nanomaterials.
Mitchell, S. L.; Hudson-Smith, N.; Sharan, D.; Haynes, C. L.; Carlson, E. E. ES: Nano, 2023
RAD-TGTs: high-throughput measurement of cellular mechanotype via rupture and delivery of DNA tension probes
Pawlak, M.R., Smiley, A.T., Ramirez, M.P., Kelly, M.D., Shamsan, G.A., Anderson, S.M., Smeester, B.A., Largaespada, D.A., Odde, D.J., Gordon, W.R., RAD-TGTs: high-throughput measurement of cellular mechanotype via rupture and delivery of DNA tension probes. Nat Commun 14, 2468 (2023).
https://doi.org/10.1038/s41467-023-38157-6
Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities
Petenkova, A.; Auger, S. A.; Lamb, J.; Quellier, D.; Carter, C.; To, O. T.; Milosevic, J.; Barghout, R.; Kugadas, A.; Lu, X.; Geddes-McAlister, J.; Fichorova, R.; Sykes, D. B.; Distefano, M. D.; Gadjeva, M. Prenylcysteine oxidase 1 like protein is required for neutrophil bactericidal activities. Nat Commun 14, 2761 (2023).
Electrostatically Regulated Active Site Assembly Governs Reactivity in Nonheme Iron Halogenases
Elizabeth R. Smithwick, R. Hunter Wilson, Sourav Chatterjee, Yu Pu, Joseph J. Dalluge, Anoop Rama Damodaran, and Ambika Bhagi-Damodaran
ACS Catalysis 2023 13 (20), 13743-13755
https://doi.org/10.1021/acscatal.3c02531
Recent progress and structural analyses of domain-selective BET inhibitors
Divakaran, A.; Harki, D. A.; Pomerantz, W. C. K. Recent Progress and Structural Analyses of Domain-Selective BET Inhibitors. Medicinal Research Reviews. 2023, 1-47.
Publication Outcomes 2018-2023:
A) CBITG collaborative papers from 2018-present involving CBITG trainers and/or trainees. B) Departmental breakdown of the 28 papers involving more than one CBITG trainer.
Fragment-Based NMR Screening of the BPTF PHD Finger Methyl Lysine Reader Leads to the First Small-Molecule Inhibitors
Buchholz, C. R.; Sneddon, M. S.; McPherson, J. E.; Das, S.; Gee, C. T.; Grillo, M. J.; Chai, S. C.; Lee, R. E.; Chen, T.; Harki, D. A.; Shelat, A. A.; Pomerantz, W. C. K. ACS Medicinal Chemistry Letters Article ASAP. 2023.
pH Effects Can Dominate Chemical Shift Perturbations in 1H,15N-HSQC NMR Spectroscopy for Studies of Small Molecule/α-Synuclein Interactions
Pandey, A. K.; Buchholz, C. R.; Nathan Kochen, N.; Pomerantz, W. C. K.; Braun, A. R.; Sachs, J. N. pH Effects Can Dominate Chemical Shift Perturbations in 1H,15N-HSQC NMR Spectroscopy for Studies of Small Molecule/α-Synuclein Interactions. ACS Chem. Neurosci. 2023, 14 (4), 800–808.
Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases
Smiley, A. T.; Tompkins, K. J.; Pawlak, M. R.; Krueger, A. J.; Evans, R. L., 3rd; Shi, K.; Aihara, H.; Gordon, W. R. Watson-Crick Base-Pairing Requirements for ssDNA Recognition and Processing in Replication-Initiating HUH Endonucleases. MBio 2023, 14 (1), e0258722.
Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability
Joaqui-Joaqui, M. A.; Maxwell, Z.; Ramakrishnam Raju, M. V.; Jiang, M.; Srivastava, K.; Shao, F.; Arriaga, E. A.; Pierre, V. C. Metallointercalators-DNA Tetrahedron Supramolecular Self-Assemblies with Increased Serum Stability. ACS Nano 2022, 16 (2), 2928–2941.
Small Molecule Inhibitors of TET Dioxygenases: Bobcat339 Activity Is Mediated by Contaminating Copper(II)
Weirath, N. A.; Hurben, A. K.; Chao, C.; Pujari, S. S.; Cheng, T.; Liu, S.; Tretyakova, N. Y. Small Molecule Inhibitors of TET Dioxygenases: Bobcat339 Activity Is Mediated by Contaminating Copper(II). ACS Med. Chem. Lett. 2022, 13 (5), 792–798.
Combining Isoprenoid Probes with Antibody Markers for Mass Cytometric Analysis of Prenylation in Single Cells
Maxwell, Z. A.; Suazo, K. F.; Brown, H. M. G.; Distefano, M. D.; Arriaga, E. A. Combining Isoprenoid Probes with Antibody Markers for Mass Cytometric Analysis of Prenylation in Single Cells. Anal. Chem. 2022, 94 (33), 11521–11528.
Engineering Biomimetic Trogocytosis with Farnesylated Chemically Self-Assembled Nanorings
Wang, Y.; Rozumalski, L.; Kilic, O.; Lichtenfels, C.; Petersberg, J.; Distefano, M. D.; Wagner, C. R. Engineering Biomimetic Trogocytosis with Farnesylated Chemically Self-Assembled Nanorings. Biomacromolecules 2022, 23 (12), 5018–5035.
Role of Protein Damage Inflicted by Dopamine Metabolites in Parkinson’s Disease: Evidence, Tools, and Outlook
Hurben, A. K.; Tretyakova, N. Y. Role of Protein Damage Inflicted by Dopamine Metabolites in Parkinson’s Disease: Evidence, Tools, and Outlook. Chem. Res. Toxicol. 2022, 35 (10), 1789–1804.
Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-heme Iron Enzymes
Wilson, R. H.; Chatterjee, S.; Smithwick, E. R.; Dalluge, J. J.; Bhagi-Damodaran, A. Role of Secondary Coordination Sphere Residues in Halogenation Catalysis of Non-Heme Iron Enzymes. ACS Catal. 2022, 12 (17), 10913–10924.
In Vivo Prenylomic Profiling in the Brain of a Transgenic Mouse Model of Alzheimer’s Disease Reveals Increased Prenylation of a Key Set of Proteins
Jeong, A.; Auger, S. A.; Maity, S.; Fredriksen, K.; Zhong, R.; Li, L.; Distefano, M. D. In Vivo Prenylomic Profiling in the Brain of a Transgenic Mouse Model of Alzheimer’s Disease Reveals Increased Prenylation of a Key Set of Proteins. ACS Chem. Biol. 2022, 17 (10), 2863–2876.
Combined Structural Analysis and Molecular Dynamics Reveal Novel Penicillin-Binding Protein Inhibition Mode with β-Lactones
Flanders, P. L.; Contreras-Martel, C.; Brown, N. W.;† Shirley, J. D.;† Martins, A.; Nauta, K. M.; Dessen, A.; Carlson, E. E.;* Ambrose. E. A.* ACS Chem. Biol. 2022, 17, 3110-3120.
Selected for Journal Cover
DEB-FAPy-dG Adducts of 1,3-Butadiene: Synthesis, Structural Characterization, and Formation in 1,2,3,4-Diepoxybutane Treated DNA
Pujari, S. S.; Jokipii Krueger, C. C.; Chao, C.; Hutchins, S.; Hurben, A. K.; Boysen, G.; Tretyakova, N. DEB-FAPy-dG Adducts of 1,3-Butadiene: Synthesis, Structural Characterization, and Formation in 1,2,3,4-Diepoxybutane Treated DNA. Chemistry 2022, 28 (3), e202103245.
Photocaged dicarbonyl probe provides spatiotemporal control over protein glycation
Hurben, A. K.; Ge, P.; Bouchard, J. L.; Doran, T. M.; Tretyakova, N. Y. Photocaged Dicarbonyl Probe Provides Spatiotemporal Control over Protein Glycation. Chem. Commun. 2022, 58 (6), 855–858.
New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition
Zahid, H.; Buchholz, C. R.; Singh, M.; Ciccone, M. F.; Chan, A.; Nithianantham, S.; Shi, K.; Aihara, H.; Fischer, M.; Schönbrunn, E.; Dos Santos, C. O.; Landry, J. W.; Pomerantz, W. C. K. New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. J. Med. Chem. 2021, 64 (18), 13902–13917.
Nonspecific Binding Correction for Single-Cell Mass Cytometric Analysis of Autophagy and Myoblast Differentiation
Brown, H. M. G.; Kuhns, M. M.; Maxwell, Z.; Arriaga, E. A. Nonspecific Binding Correction for Single-Cell Mass Cytometric Analysis of Autophagy and Myoblast Differentiation. Anal. Chem. 2021, 93 (3), 1401–1408.
Translesion Synthesis Past 5-Formylcytosine-Mediated DNA–Peptide Cross-Links by hPolη Is Dependent on the Local DNA Sequence
Thomforde, J.; Fu, I.; Rodriguez, F.; Pujari, S. S.; Broyde, S.; Tretyakova, N. Translesion Synthesis Past 5-Formylcytosine-Mediated DNA-Peptide Cross-Links by hPolη Is Dependent on the Local DNA Sequence. Biochemistry 2021, 60 (23), 1797–1807.
4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity
Cui, H.; Carlson, A. S.; Schleiff, M. A.; Divakaran, A.; Johnson, J. A.; Buchholz, C. R.; Zahid, H.; Vail, N. R.; Shi, K.; Aihara, H.; Harki, D. A.; Miller, G. P.; Topczewski, J. J.; Pomerantz, W. C. K. 4-Methyl-1,2,3-Triazoles as N-Acetyl-Lysine Mimics Afford Potent BET Bromodomain Inhibitors with Improved Selectivity. J. Med. Chem. 2021, 64 (14), 10497–10511.
Effects of GSTT1 Genotype on the Detoxification of 1,3-Butadiene Derived Diepoxide and Formation of Promutagenic DNA–DNA Cross-Links in Human Hapmap Cell Lines
Boysen, G.; Arora, R.; Degner, A.; Vevang, K. R.; Chao, C.; Rodriguez, F.; Walmsley, S. J.; Erber, L.; Tretyakova, N. Y.; Peterson, L. A. Effects of GSTT1 Genotype on the Detoxification of 1,3-Butadiene Derived Diepoxide and Formation of Promutagenic DNA-DNA Cross-Links in Human Hapmap Cell Lines. Chem. Res. Toxicol. 2021, 34 (1), 119–131.
19F NMR viewed through two different lenses: ligand-observed and protein-observed 19F NMR applications for fragment-based drug discovery
Buchholz, C. R.; Pomerantz, W. C. K. 19F NMR Viewed through Two Different Lenses: Ligand-Observed and Protein-Observed 19F NMR Applications for Fragment-Based Drug Discovery. RSC Chem Biol 2021, 2 (5), 1312–1330.
Proteome-Wide Profiling of Cellular Targets Modified by Dopamine Metabolites Using a Bio-Orthogonally Functionalized Catecholamine
Hurben, A. K.; Erber, L. N.; Tretyakova, N. Y.; Doran, T. M. Proteome-Wide Profiling of Cellular Targets Modified by Dopamine Metabolites Using a Bio-Orthogonally Functionalized Catecholamine. ACS Chem. Biol. 2021, 16 (11), 2581–2594.
Journeying through the Field of Medicinal Chemistry: Perspectives from Graduate Researchers
Koerperich, Z. M.; Kennelly, S. A.; McDermott, C. M.; Bentz, N. M.; Buchholz, C. R.; Fuller, J. L.; Kilic, O.; Ge, P. Journeying through the Field of Medicinal Chemistry: Perspectives from Graduate Researchers. J. Med. Chem. 2020, 63 (5), 1882–1891.
6-phenylpyrrolocytosine as a fluorescent probe to examine nucleotide flipping catalyzed by a DNA repair protein
Kotandeniya, D.; Rogers, M. S.; Fernandez, J.; Kanugula, S.; Hudson, R. H. E.; Rodriguez, F.; Lipscomb, J. D.; Tretyakova, N. 6-Phenylpyrrolocytosine as a Fluorescent Probe to Examine Nucleotide Flipping Catalyzed by a DNA Repair Protein. Biopolymers 2021, 112 (1), e23405.
Chronic Exposure to Complex Metal Oxide Nanoparticles Elicits Rapid Resistance in Shewanella oneidensis MR-1
Mitchell, S. L.; Hudson-Smith, N. V.; Cahill, M. S.; Reynolds, B. N.; Frand, S. D.; Green, C. M.; Wang, C.; Hang, M. N.; Tapia Hernandez, R.; Hamers, R. J.; Feng, Z. V.; Haynes, C. L.; Carlson, E. E. Chem. Sci. 2019, 10, 9768-9781.
**Press releases from NSF, AAAS, Chemistry World, UMN, and Star Tribune.
Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase
Zhang, Y.; Auger, S.; Schaefer, J. V.; Plückthun, A.; Distefano, M. D. Site-Selective Enzymatic Labeling of Designed Ankyrin Repeat Proteins Using Protein Farnesyltransferase. In Bioconjugation: Methods and Protocols; Massa, S., Devoogdt, N., Eds.; Springer New York: New York, NY, 2019; pp 207–219.
Biological Impact of Lithium Intercalating Complex Metal Oxides to Model Bacterium Bacilis subtillus
Feng, Z. V.; Miller, B.; Linn, T. G.; Pho, T.; Hoang, K. N. L.; Hang, M. N.; Mitchell, S. L.; Tapia Hernandez, R.; Carlson, E. E.; Hamers, R. J. Bacillus subtilis. Environ. Sci.: Nano 2019, 6, 305-314.
Tiny Things with Enormous Impact: Nanotechnology in the Fight Against Infectious Disease
Mitchell, S. L. and Carlson, E. E. ACS Infect. Dis. 2018, 12, 1432-1435. Invited View Point.