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Trader Lab Publications
27) Loy, C.A.; Trader, D.J. Caged aminoluciferin probe for bioluminescent immunoproteasome activity analysis, RSC Chemical Biology, 2024, Advance Article, DOI: https://doi.org/10.1039/D4CB00148F
26) Loy, C.A.; Trader, D.J. Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement, Molecules, 2024, In Press, https://doi.org/10.3390/molecules29143356
25) Salazar, A; Kragness, K.A.; Feleciano, D.; Trader, D.J. AM404 Analogs as Activators of the 20S Isoform of the Human Proteasome, ChemBiochem, 2024, In Press, https://doi.org/10.1002/cbic.202400284
24) Kragness, K.A.; Trader, D.J. The Role of the Proteasome in Limiting Cell Stress Associated with Protein Accumulation, Isr. J. Chem., 2023, e202300120.
https://doi.org/10.1002/ijch.202300120
**Contributed as a perspective in the IJC Special Issue:Gettingin Shape:Targeting the Molecular Etiology of Protein Folding Diseases.
23) Loy, C.A.; Muli, C.M.; Ali, E.M.H.; Xie, D.; Ahmed, M.H.; Post, C.B.; Trader, D.J. Discovery of a non-covalent ligand for Rpn-13, a therapeutic target for hematological cancers, Bioorg. Med. Chem. Lett., 2023, 85, 129485
https://doi.org/10.1016/j.bmcl.2023.129485
22) Muli, C.M.; Trader, D.J. 20S proteasome hydrolysis of LLVY substrates to determine preferences for moieties in its primed substrate channel, Bioorg. Med. Chem. Lett., 2023, 85, 129233. https://www.sciencedirect.com/science/article/pii/S0960894X23001117
21) Halder, S.; Macatangay, N.J.; Zerfas, B.L.; Salazar-Chaparro, A.F.; Trader, D.J. Oleic Amide Derivatives as Small Molecule Stimulators of the Human Proteasome’s Core Particle, RSC Med. Chem., 2022, 13, 1077-1081.
20) Salazar-Chaparro, A.; Halder, S.; Trader, D.J. Synthesis and Application of a Clickable Epoxomicin-Based Probe for Proteasome Activity Analysis, Curr. Protoc. Chem. Biol, 2022, 2 (7), e490.
19) Salazar-Chaparro, A.; Halder, S.; Maresh, M.E.; Trader, D.J. Solid-Phase Synthesis and Application of a Clickable Version of Epoxomicin for Proteasome Activity Analysis, ChemBiochem, 2022, 23 (7), e202100710. https://doi.org/10.1002/cbic.202100710
18) Maresh, M.E.; Chen, P; Hazbun, T.R.; Trader, D.J. A Yeast Chronological Lifespan Assay to Assess Activity of Proteasome Stimulators, ChemBiochem, 2021, 22 (15), 2553-2560. https://doi.org/10.1002/cbic.202100117
17) Tian, W.; Maresh, M.E.; Trader, D.J. Approaches to Evaluate the Impact of a Small Molecule Binder to a Non-catalytic Site of the Proteasome, ChemBiochem, 2021, 22 (11), 1961-1965. https://doi.org/10.1002/cbic.202100023
**Invited for Special Collection on Translational Chemical Biology
16) Maresh, M.E.; Zerfas, B.L.; Wuthrich, B.S.; Trader, D.J. Identification of a Covalent Binder to the Oncoprotein Gankyrin Using a NIR-Based OBOC Screening Method, RSC Advances, 2021, 11, 12794-12801.
**Invited for Emerging Investigators Series
15) Maresh, M.E.; Salazar-Chaparro, A.F.; Trader, D.J. Methods for the Discovery of Small Molecules to Monitor and Perturb the Activity of the Human Proteasome, Future Med. Chem., ASAP, 2020.
https://www.future-science.com/doi/10.4155/fmc-2020-0288
14) Zerfas, B.L.; Coleman, R.A.; Salazar-Chaprro, A.; Macatangay, N.J.; Trader, D.J. Fluorescent Probes with Unnatural Amino Acids to Monitor Proteasome Activity in Real-Time, ACS Chem. Biol. 2020, 15, 2588-2596.
https://pubs.acs.org/doi/full/10.1021/acschembio.0c00634
13) Coleman, R.A.; Mohallem, R.; Aryal, U.K.; Trader, D.J. Protein Degradation Profile Reveals Dynamic Nature of 20S CP Small Molecule Stimulation, RSC Chem. Biol., 2020, In Press, https://doi.org/10.1039/D0CB00191K
12) Tian, W.; Trader, D.J. Discovery of a Small Molecule Probe of Rpn-6, an Essential Subunit of the 26S Proteasome, ACS Chemical Biology, 2020, 15 (2), 554-561.
https://pubs.acs.org/doi/full/10.1021/acschembio.9b01019
11) Zerfas, B.L.; Maresh, M.E.; Trader, D.J. The Immunoproteasome: An Emerging Target in Cancer, Autoimmune, Neurological Disorders,
J. Med. Chem., 2020, 63 (5), 1841-1858.
https://doi.org/10.1021/acs.jmedchem.9b01226
10) Zerfas, B.L.; Trader, D.J. Synthesis and Application of an Activity-Based Peptide-Peptoid Hybrid Probe for the Immunoproteasome, Current Protocols in Chemical Biology, 2019, e76.
https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpch.76
9) Coleman, R.A.; Trader, D.J. Methods to Discover and Evaluate Proteasome Small Molecule Simulators, Molecules, 2019, 24, 2341.
https://www.mdpi.com/1420-3049/24/12/2341
8) Zerfas, B.L.; Trader, D.J. Monitoring the Immunoproteasome in Live Cells Using an Activity-Based Peptide-Peptoid Hybrid Probe. J. Am. Chem. Soc. 2019, 141 (13), 5252-5260.
https://pubs.acs.org/doi/10.1021/jacs.8b12873
7) Muli, C.S.; Tian, W.; Trader, D.J. Small Molecule Inhibitors of the Proteasome's Regulatory Particle, ChemBioChem- ChemBioTalents Issue, 2019, 20 (14), 1739-1753.
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201900017.
6) Maresh, M.E.; Trader, D.J. Development of a Method to Prioritize Protein-Ligand Pairs on Beads Using Protein Conjugated to a Near-IR Dye, ACS Comb. Sci., 2019, 21 (3), 223-228.
https://pubs.acs.org/doi/10.1021/acscombsci.8b00165.
5)Cassell, R.J.; Mores, K.L.; Zerfas, B.L.; Mahmoud, A,H.; Lill, M.A.; Trader, D.J.; van Rijn, R.M. Rubiscolins are naturally occuring G protein biased delta opioid receptor peptides, Eur Neuropsychopharmacol., 2019, 29 (3), 450-456.
https://www.sciencedirect.com/science/article/pii/S0924977X18320042?via%3Dihub
4) Coleman, R.A.; Muli, C.S.; Zhao, Y.; Bhardwaj, A.; Newhouse, T.R.; Trader, D.J. Analysis of Chain Length, Substitution Patterns, and Unsaturation of AM-404 Derivatives as 20S Proteasome Stimulators, Bioorganic Med. Chem. Lett., 2019, 29 (3), 420-423.
https://doi.org/10.1016/j.bmcl.2018.12.030
3) Coleman, R.A.; Trader, D.J. All About the Core: A Therapeutic Strategy to Prevent Protein Accumulation with Proteasome Core Particle Stimulators, ACS Pharmacol. Transl. Sci., 2018, 1 (2), 140-142.
https://pubs.acs.org/doi/10.1021/acsptsci.8b00042
2) Coleman, R.A.; Trader, D.J. A sensitive high-throughput screening method for identifying small molecule stimulators of the core particle of the proteasome, Current Protocols in Chemical Biology, 2018, https://doi.org/10.1002/cpch.52
1) Coleman, R.A.; Trader, D.J. Development and Application of a Sensitive Peptide Reporter to Discover 20S Proteasome Stimulators, ACS Comb. Sci., 2018, 20 (5), 269–276.
https://pubs.acs.org/doi/10.1021/acscombsci.7b00193
26) Loy, C.A.; Trader, D.J. Primed for Interactions: Investigating the Primed Substrate Channel of the Proteasome for Improved Molecular Engagement, Molecules, 2024, In Press, https://doi.org/10.3390/molecules29143356
25) Salazar, A; Kragness, K.A.; Feleciano, D.; Trader, D.J. AM404 Analogs as Activators of the 20S Isoform of the Human Proteasome, ChemBiochem, 2024, In Press, https://doi.org/10.1002/cbic.202400284
24) Kragness, K.A.; Trader, D.J. The Role of the Proteasome in Limiting Cell Stress Associated with Protein Accumulation, Isr. J. Chem., 2023, e202300120.
https://doi.org/10.1002/ijch.202300120
**Contributed as a perspective in the IJC Special Issue:Gettingin Shape:Targeting the Molecular Etiology of Protein Folding Diseases.
23) Loy, C.A.; Muli, C.M.; Ali, E.M.H.; Xie, D.; Ahmed, M.H.; Post, C.B.; Trader, D.J. Discovery of a non-covalent ligand for Rpn-13, a therapeutic target for hematological cancers, Bioorg. Med. Chem. Lett., 2023, 85, 129485
https://doi.org/10.1016/j.bmcl.2023.129485
22) Muli, C.M.; Trader, D.J. 20S proteasome hydrolysis of LLVY substrates to determine preferences for moieties in its primed substrate channel, Bioorg. Med. Chem. Lett., 2023, 85, 129233. https://www.sciencedirect.com/science/article/pii/S0960894X23001117
21) Halder, S.; Macatangay, N.J.; Zerfas, B.L.; Salazar-Chaparro, A.F.; Trader, D.J. Oleic Amide Derivatives as Small Molecule Stimulators of the Human Proteasome’s Core Particle, RSC Med. Chem., 2022, 13, 1077-1081.
20) Salazar-Chaparro, A.; Halder, S.; Trader, D.J. Synthesis and Application of a Clickable Epoxomicin-Based Probe for Proteasome Activity Analysis, Curr. Protoc. Chem. Biol, 2022, 2 (7), e490.
19) Salazar-Chaparro, A.; Halder, S.; Maresh, M.E.; Trader, D.J. Solid-Phase Synthesis and Application of a Clickable Version of Epoxomicin for Proteasome Activity Analysis, ChemBiochem, 2022, 23 (7), e202100710. https://doi.org/10.1002/cbic.202100710
18) Maresh, M.E.; Chen, P; Hazbun, T.R.; Trader, D.J. A Yeast Chronological Lifespan Assay to Assess Activity of Proteasome Stimulators, ChemBiochem, 2021, 22 (15), 2553-2560. https://doi.org/10.1002/cbic.202100117
17) Tian, W.; Maresh, M.E.; Trader, D.J. Approaches to Evaluate the Impact of a Small Molecule Binder to a Non-catalytic Site of the Proteasome, ChemBiochem, 2021, 22 (11), 1961-1965. https://doi.org/10.1002/cbic.202100023
**Invited for Special Collection on Translational Chemical Biology
16) Maresh, M.E.; Zerfas, B.L.; Wuthrich, B.S.; Trader, D.J. Identification of a Covalent Binder to the Oncoprotein Gankyrin Using a NIR-Based OBOC Screening Method, RSC Advances, 2021, 11, 12794-12801.
**Invited for Emerging Investigators Series
15) Maresh, M.E.; Salazar-Chaparro, A.F.; Trader, D.J. Methods for the Discovery of Small Molecules to Monitor and Perturb the Activity of the Human Proteasome, Future Med. Chem., ASAP, 2020.
https://www.future-science.com/doi/10.4155/fmc-2020-0288
14) Zerfas, B.L.; Coleman, R.A.; Salazar-Chaprro, A.; Macatangay, N.J.; Trader, D.J. Fluorescent Probes with Unnatural Amino Acids to Monitor Proteasome Activity in Real-Time, ACS Chem. Biol. 2020, 15, 2588-2596.
https://pubs.acs.org/doi/full/10.1021/acschembio.0c00634
13) Coleman, R.A.; Mohallem, R.; Aryal, U.K.; Trader, D.J. Protein Degradation Profile Reveals Dynamic Nature of 20S CP Small Molecule Stimulation, RSC Chem. Biol., 2020, In Press, https://doi.org/10.1039/D0CB00191K
12) Tian, W.; Trader, D.J. Discovery of a Small Molecule Probe of Rpn-6, an Essential Subunit of the 26S Proteasome, ACS Chemical Biology, 2020, 15 (2), 554-561.
https://pubs.acs.org/doi/full/10.1021/acschembio.9b01019
11) Zerfas, B.L.; Maresh, M.E.; Trader, D.J. The Immunoproteasome: An Emerging Target in Cancer, Autoimmune, Neurological Disorders,
J. Med. Chem., 2020, 63 (5), 1841-1858.
https://doi.org/10.1021/acs.jmedchem.9b01226
10) Zerfas, B.L.; Trader, D.J. Synthesis and Application of an Activity-Based Peptide-Peptoid Hybrid Probe for the Immunoproteasome, Current Protocols in Chemical Biology, 2019, e76.
https://currentprotocols.onlinelibrary.wiley.com/doi/abs/10.1002/cpch.76
9) Coleman, R.A.; Trader, D.J. Methods to Discover and Evaluate Proteasome Small Molecule Simulators, Molecules, 2019, 24, 2341.
https://www.mdpi.com/1420-3049/24/12/2341
8) Zerfas, B.L.; Trader, D.J. Monitoring the Immunoproteasome in Live Cells Using an Activity-Based Peptide-Peptoid Hybrid Probe. J. Am. Chem. Soc. 2019, 141 (13), 5252-5260.
https://pubs.acs.org/doi/10.1021/jacs.8b12873
7) Muli, C.S.; Tian, W.; Trader, D.J. Small Molecule Inhibitors of the Proteasome's Regulatory Particle, ChemBioChem- ChemBioTalents Issue, 2019, 20 (14), 1739-1753.
https://onlinelibrary.wiley.com/doi/abs/10.1002/cbic.201900017.
6) Maresh, M.E.; Trader, D.J. Development of a Method to Prioritize Protein-Ligand Pairs on Beads Using Protein Conjugated to a Near-IR Dye, ACS Comb. Sci., 2019, 21 (3), 223-228.
https://pubs.acs.org/doi/10.1021/acscombsci.8b00165.
5)Cassell, R.J.; Mores, K.L.; Zerfas, B.L.; Mahmoud, A,H.; Lill, M.A.; Trader, D.J.; van Rijn, R.M. Rubiscolins are naturally occuring G protein biased delta opioid receptor peptides, Eur Neuropsychopharmacol., 2019, 29 (3), 450-456.
https://www.sciencedirect.com/science/article/pii/S0924977X18320042?via%3Dihub
4) Coleman, R.A.; Muli, C.S.; Zhao, Y.; Bhardwaj, A.; Newhouse, T.R.; Trader, D.J. Analysis of Chain Length, Substitution Patterns, and Unsaturation of AM-404 Derivatives as 20S Proteasome Stimulators, Bioorganic Med. Chem. Lett., 2019, 29 (3), 420-423.
https://doi.org/10.1016/j.bmcl.2018.12.030
3) Coleman, R.A.; Trader, D.J. All About the Core: A Therapeutic Strategy to Prevent Protein Accumulation with Proteasome Core Particle Stimulators, ACS Pharmacol. Transl. Sci., 2018, 1 (2), 140-142.
https://pubs.acs.org/doi/10.1021/acsptsci.8b00042
2) Coleman, R.A.; Trader, D.J. A sensitive high-throughput screening method for identifying small molecule stimulators of the core particle of the proteasome, Current Protocols in Chemical Biology, 2018, https://doi.org/10.1002/cpch.52
1) Coleman, R.A.; Trader, D.J. Development and Application of a Sensitive Peptide Reporter to Discover 20S Proteasome Stimulators, ACS Comb. Sci., 2018, 20 (5), 269–276.
https://pubs.acs.org/doi/10.1021/acscombsci.7b00193
Publications Prior To Trader Lab
2006-2017
10. Trader, D. J.; Simanski, S.; Kodadek, T. Establishment of a Suite of Assays that Support the Discovery of Proteasome Agonists. Biochim. Biophys. Acta, 2017, 1861, 892-899
9. Trader, D. J.; Simanski, S.; Kodadek, T. A Reversible and Highly Selective Inhibitor of the Proteasomal Ubiquitin Receptor Rpn13 is Toxic to Multiple Myeloma Cells. J. Am. Chem. Soc., 2015, 137, 6312-6319.
**Highlighted in: Nature, 2015, 521, May 7, pg. 8
8. Trader, D. J. and Carlson, E. E. Chemoselective Enrichment as a Tool to Increase Access to Bioactive Natural Products: Case Study Borrelidin. Bioorg. Med. Chem. Lett., 2015, 25, 4767-4769. 25th Anniversary Issue Entitled, "Recent Advances in Medicinal Chemistry and Chemical Biology.”
7. Trader, D. J. and Carlson, E. E. Towards the Development of Solid Supported Reagents for Separation of Alcohol-Containing Compounds by Steric Environment. Tetrahedron, 2014, 70, 4191-4196. Special Issue to Honor Sarah Reisman for Receipt of the Tetrahedron Young Investigator Award.
6. Trader, D. J. and Carlson, E. E. Taming of a Superbase for Selective Phenol Desilylation and Natural Product Discovery. J. Org. Chem., 2013, 78, 7349-7355.
5. Sidebottom, A. M.; Johnson, A. R.; Karty, J. A.; Trader, D. J. and Carlson, E. E. Integrated Metabolomics Approach Facilitates Discovery of an Unpredicted Natural Product Suite from Streptomyces coelicolor M145. ACS Chem. Biol. 2013, 8, 2009-2016.
4. Trader, D. J. and Carlson, E. E. Chemoselective Hydroxyl Group Transformation: An Elusive Target. Mol. Bio. Sys. 2012, 8, 2484-2493. Invited Review in Emerging Investigators Themed Issue.**Selected as Molecular BioSystems HOT Article and highlighted on their blog, http://blogs.rsc.org/mb/ (7/17/2012)
3. Trader, D. J. and Carlson, E. E. Siloxyl Ether-Functionalized Resins for Chemoselective Capture of Carboxylic Acids. Org. Lett. 2011, 13, 5652-5655.
2. Odendaal, A. Y.†; Trader, D. J.†; Carlson, E. E. Chemoselective Enrichment for Natural Products Discovery. Chem. Sci. 2011, 2, 760-764.**Highlighted in: Chem. & Eng. News, 2011, 89, Feb 14, 34-35 and Chemistry World (http://www.rsc.org/chemistryworld/News/2011/February/15021101.asp)
1. Gibbs, K.; Trader, D. J.; O’Brien, L. C.; O’Brien, J. J. Fourier Transform Spectroscopy of NiCl. Identification of the [10.3] 4. Fourier. J. Mol. Spectrosc. 2006, 240, 64-68.This journal does not appear in the PubMed database.
9. Trader, D. J.; Simanski, S.; Kodadek, T. A Reversible and Highly Selective Inhibitor of the Proteasomal Ubiquitin Receptor Rpn13 is Toxic to Multiple Myeloma Cells. J. Am. Chem. Soc., 2015, 137, 6312-6319.
**Highlighted in: Nature, 2015, 521, May 7, pg. 8
8. Trader, D. J. and Carlson, E. E. Chemoselective Enrichment as a Tool to Increase Access to Bioactive Natural Products: Case Study Borrelidin. Bioorg. Med. Chem. Lett., 2015, 25, 4767-4769. 25th Anniversary Issue Entitled, "Recent Advances in Medicinal Chemistry and Chemical Biology.”
7. Trader, D. J. and Carlson, E. E. Towards the Development of Solid Supported Reagents for Separation of Alcohol-Containing Compounds by Steric Environment. Tetrahedron, 2014, 70, 4191-4196. Special Issue to Honor Sarah Reisman for Receipt of the Tetrahedron Young Investigator Award.
6. Trader, D. J. and Carlson, E. E. Taming of a Superbase for Selective Phenol Desilylation and Natural Product Discovery. J. Org. Chem., 2013, 78, 7349-7355.
5. Sidebottom, A. M.; Johnson, A. R.; Karty, J. A.; Trader, D. J. and Carlson, E. E. Integrated Metabolomics Approach Facilitates Discovery of an Unpredicted Natural Product Suite from Streptomyces coelicolor M145. ACS Chem. Biol. 2013, 8, 2009-2016.
4. Trader, D. J. and Carlson, E. E. Chemoselective Hydroxyl Group Transformation: An Elusive Target. Mol. Bio. Sys. 2012, 8, 2484-2493. Invited Review in Emerging Investigators Themed Issue.**Selected as Molecular BioSystems HOT Article and highlighted on their blog, http://blogs.rsc.org/mb/ (7/17/2012)
3. Trader, D. J. and Carlson, E. E. Siloxyl Ether-Functionalized Resins for Chemoselective Capture of Carboxylic Acids. Org. Lett. 2011, 13, 5652-5655.
2. Odendaal, A. Y.†; Trader, D. J.†; Carlson, E. E. Chemoselective Enrichment for Natural Products Discovery. Chem. Sci. 2011, 2, 760-764.**Highlighted in: Chem. & Eng. News, 2011, 89, Feb 14, 34-35 and Chemistry World (http://www.rsc.org/chemistryworld/News/2011/February/15021101.asp)
1. Gibbs, K.; Trader, D. J.; O’Brien, L. C.; O’Brien, J. J. Fourier Transform Spectroscopy of NiCl. Identification of the [10.3] 4. Fourier. J. Mol. Spectrosc. 2006, 240, 64-68.This journal does not appear in the PubMed database.
Patents
3. Carlson, E. E.; Trader, D. J.; Sidebottom, A. M. Design and Application of a Tag for Discovery of Natural Products Containing an Alkyne. U.S. Patent Number 20,150,240,006 A1, Issued August 27, 2015.
2. Carlson, E. E. and Trader, D. J. Siloxyl Ether Reagents for Chemoselective Reaction with Carboxylic Acids. U.S. Patent Number 20,140,107,328 A1, Issued April 17, 2014.
1. Carlson, E. E.; Trader, D. J.; Odendaal, A. Y. Chemoselective Enrichment for Compound Isolation. U.S. Patent Number 9,079,983 B2, Issued July 14, 2015.
2. Carlson, E. E. and Trader, D. J. Siloxyl Ether Reagents for Chemoselective Reaction with Carboxylic Acids. U.S. Patent Number 20,140,107,328 A1, Issued April 17, 2014.
1. Carlson, E. E.; Trader, D. J.; Odendaal, A. Y. Chemoselective Enrichment for Compound Isolation. U.S. Patent Number 9,079,983 B2, Issued July 14, 2015.
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