Publications

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