Publications

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

https://doi.org/10.1021/acssynbio.4c00188  

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 

https://doi.org/10.1021/acs.jmedchem.3c01831  

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.

 https://doi.org/10.1128/aem.00548-23

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

https://doi.org/10.1021/acs.biochem.3c00306 

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.

https://doi.org/10.1016/j.jbc.2023.104698

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 

https://doi.org/10.1039/D3EN00420A 

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). 

https://doi.org/10.1038/s41467-023-38447-z 

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.

 https://doi.org/10.1002/med.21942

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.

https://doi.org/10.1021/acsmedchemlett.3c00343

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.

https://doi.org/10.1021/acschemneuro.2c00782

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.

https://doi.org/10.1128/mbio.02587-22

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.

https://doi.org/10.1021/acsnano.1c10084

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.

https://doi.org/10.1021/acsmedchemlett.1c00677

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.

https://doi.org/10.1021/acs.analchem.2c01509

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.

https://doi.org/10.1021/acs.biomac.2c00837

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.

https://doi.org/10.1021/acs.chemrestox.2c00193

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.

https://doi.org/10.1021/acscatal.2c00954

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.

https://doi.org/10.1021/acschembio.2c00486

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.

https://doi.org/10.1021/acschembio.2c00503 

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.

https://doi.org/10.1002/chem.202103245

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.

https://doi.org/10.1039/D1CC06651J

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.

https://doi.org/10.1021/acs.jmedchem.1c01294

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.

https://doi.org/10.1021/acs.analchem.0c03211

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.

https://doi.org/10.1021/acs.biochem.1c00130

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.

https://doi.org/10.1021/acs.jmedchem.1c00933

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.

https://doi.org/10.1021/acs.chemrestox.0c00376

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.

https://doi.org/10.1039/D1CB00085C

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.

https://doi.org/10.1021/acschembio.1c00629

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.

https://doi.org/10.1021/acs.jmedchem.9b01309

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.

https://doi.org/10.1002/bip.23405

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.

https://dx.doi.org/10.1039/C9SC01942A

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.

https://dx.doi.org/10.1039/C8EN00995C

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.

https://dx.doi.org/10.1021/acsinfecdis.8b00138