Chemistry at Illinois University of Illinois at Urbana-Champaign

Paul J. Hergenrother

Kenneth Rinehart Jr. Endowed Chair in
natural products chemistry
Professor of chemistry
Affiliate, Department of Biochemistry

Professor Hergenrother received his B.S. in chemistry from the University of Notre Dame in 1994. He went on to the University of Texas at Austin and obtained his Ph.D. in 1999; during this time Paul was the recipient of an American Chemical Society graduate student fellowship and the Roche Award for Excellence in Organic Chemistry. After an American Cancer Society post-doctoral fellowship at Harvard University, he joined the faculty at Illinois in 2001. His research interests are in the areas of synthetic organic chemistry, chemical biology, and biochemistry.


The overarching goal of our research is to use small organic compounds to identify novel cellular targets that can be exploited in the treatment of diseases including cancer, neurodegeneration, and drug-resistant bacteria. The compounds used to validate these novel drug targets are identified through a variety of approaches, including natural product synthesis, combinatorial chemistry, structure-based design, and high-throughput screening. In the process, novel methods for the synthesis of various chemical building blocks and for biological assays often need to be developed. In addition, we work closely with the local medical community and perform tests directly on patient samples.

Novel anti-cancer targets.

There are currently no treatments for certain cancers such as colon cancer and late-stage malignant melanoma. We have synthesized a series of compounds, the triphenylmethylamides (TPMAs), which powerfully induce programmed cell death in melanoma and are comparatively less toxic to non-cancerous cells. The TPMAs appear to function via a novel biochemical mechanism, and cause arrest of cancer cells in the G1 phase of the cell cycle. In a separate series of experiments, through high-throughput screening and combinatorial synthesis we have identified compounds that directly induce programmed cell death in a variety of cancer cells; these compounds are currently being tested against patient samples and in mouse models.

Novel targets for drug-resistant bacteria.

Every year 90,000 people in the U.S. alone die from bacterial infections they acquire at hospitals. Many of these bacteria become resistant to antibiotics by taking up a plasmid, a small piece of circular DNA that encodes for the proteins that mediate antibiotic resistance. We have recently identified anti-plasmid agents—compounds that inhibit plasmid replication and thus sensitize bacteria to traditional antibiotics. We have focused sharply on Vancomycin-Resistant Enterococci (VRE); we have obtained clinical VRE isolates from local medical centers and are defining plasmid-encoded resistance in VRE. This work has spawned a large and general effort in the laboratory to develop a paradigm for small molecule-RNA binding. We have identified small molecule modules that bind tightly and specifically to defined regions of RNA secondary structure, including RNA hairpin loops and bulges. We are connecting such modules to target individual mRNAs in the cell with exquisite affinity and selectivity.


Hicklin, R. W.; Lopez-Silva, T. L.; Hergenrother, P. J. “Synthesis of Bridged Oxa-Fenestranes from Pleuromutilin” Angew. Chem. Int. Ed. 2014, in press pub on web 7/19/2014 DOI: 10.1002/anie.201404765/abstract

Botham, R. C.; Fan, T. M.; Im, I.; Borst, L. B; Dirikolu, L.; Hergenrother, P. J. “Dual Small-Molecule Targeting of Procaspase-3 Dramatically Enhances Zymogen Activation and Anticancer Activity” J. Am. Chem. Soc. 2014, 136, 1312-1319.

Rafferty, R. J.; Hicklin, R. W.; Maloof, K. A., Hergenrother, P.J. “Synthesis of Complex and Diverse Compounds through Ring Distortion of Abietic Acid” Angew. Chem. 2014, 53, 220-224.

Parkinson, E. I.; Bair, J. S.; Cismesia, M.; Hergenrother, P. J. “Efficient NQO1 Substrates are Potent and Selective Anticancer Agents” ACS Chem. Biol. 2013, 8, 2173-2183.

Granger, B. A.; Jewett, I, T.; Butler, J. D.; Hua, B.; Knezevic, C. E.; Parkinson, E. I.; Hergenrother, P. J.; Martin, S. F. “Synthesis of (+/-)-Actinophyllic Acid and Analogs:  Applications of Cascade Reactions and Diverted Total Synthesis” J. Am. Chem. Soc. 2013, 135, 12984-12986.

Huigens, R. W.; Morrison, K. C.; Hicklin, R. W.; Flood, T. A.; Richter, M. F.; Hergenrother, P. J. “A Ring Distortion Strategy to Construct Stereochemically Complex and Structurally Diverse Compounds from Natural Products” Nature Chem. 2013, 5, 195-202.

Dunstan, M. S.; Barkauskaite, E.; Lafite, P.; Knezevic, C. E.; Hergenrother, P. J.; Leys, D.; Ahel, I. “Structure and Mechanism of a Canonical Poly(ADP-Ribose) Glycohydrolase” Nature Comm. 2012, 3, 878.

Huang, X.; Dong, Y.; Bey, E. A.; Kilgore, J. A.; Bair, J. S.; Li, L.-S.; Patel, M.; Parkinson, E. I.; Wang, Y.; Williams, N. S.; Gao, J.; Hergenrother, P. J.; Boothman, D. A. “An NQO1 Substrate with Potent Antitumor Activity that Selectively Kills by PARP1-Induced Programmed Necrosis” Cancer Res. 2012, 72, 3038-3047.

Finch, K. E.; Knezevic, C. E.; Nottbohm, A. C.; Partlow, K. C. Hergenrother, P. J. “Selective Small Molecule Inhibition of Poly(ADP-Ribose) Glycohydrolase (PARG)” ACS Chem. Biol. 2012, 7, 563-570.

Williams, J. J.; Hergenrother, P. J. “Artificial Activation of Toxin-Antitoxin Systems as an Antibacterial Strategy” Trends Microbiol. 2012, 20, 291-298.

Hsu, D. C.; Roth, H. S.; West, D. C.; Botham, R. C.; Novotny, C. J.; Schmid, S. C.; Hergenrother, P. J. "Parallel Synthesis and Biological Evaluation of 837 Analogues of Procaspase-Activating Compound 1 (PAC-1)" ACS Combi. Sci. 2012, 14, 44-50.

Morrison, Karen C.; Hergenrother, P. J. "Whole Cell Microtubule Analysis by Flow Cytometry" Anal. Biochem. 2012, 420, 26-32.

Williams, J. J.; Halvorsen, E. M.; Dwyer, E. M.; DiFazio, R. M.; Hergenrother, P. J. "Toxin-Antitoxin (TA) Systems are Prevalent and Transcribed in Clinical Isolates of Pseudomonas aeruginosa and Methicillin-Resistant Staphylococcus aureus" FEMS Microbiol. Lett. 2011, 322, 41-50.

Granchi, C.; Roy, S.; Giacomelli, C.; Macchia, M.; Tuccinardi, T.; Martinelli, A.; Lanza, M.; Betti, L.; Giannaccini, G.; Lucacchini, A.; Funel, N.; Leon, L. G.; Giovannetti, E.; Peters, G. J.; Palchaudhuri, R.; Calvaresi, E. C.; Hergenrother, P. J.; Minutolo, F. "Discovery of N-Hydroxyindole-Based Inhibitors of Human Lactate Dehydrogenase Isoform A (LDH-A) as Starvation Agents Against Cancer Cells" J. Med. Chem. 2011, 54, 1599-1612.

Halvorsen, E. M.; Williams, J. J.; Bhimani, A. J.; Billings, E. A.; Hergenrother, P. J. "Txe, an Endoribonuclease of the Enterococcal Axe-Txe Toxin-Antitoxin System, cleaves mRNA and inhibits protein synthesis" Microbiology, 2011, 157, 387-397.

Palchaudhuri, R.; Hergenrother, P. J. "Transcript Profiling and RNA Interference as Tools to Identify Small Molecule Mechanisms and Therapeutic Potential" ACS Chem. Biol. 2011, 6, 21-33.

Hoyt, M.T.; Palchaudhuri, R.; Hergenrother, P. J. "Cribostatin 6 Induces Death in Cancer Cells Through a Reactive Oxygen Species (ROS)-Mediated Mechanism" Invest. New Drugs 2011, 29, 562-573.

Heeres, J. T.; Hergenrother, P. J. "High-Throughput Screening for Modulators of Protein-Protein Interactions: Use of Photonic Crystal Biosensors and Complementary Technologies" Chem. Soc. Rev. 2011, 40, 4398-4410.

Peterson, Q. P.; Hsu, D. C.; Novotny, C. J.; West, D. C.; Kim, D.; Schmit, J. M.; Dirikolu, L.; Hergenrother, P. J.; Fan, T. M. "Discovery and Canine Preclinical Assessment of a Nontoxic Procaspase-3 Activating Compound" Cancer Res.2010, 70, 7232-7241.

Leslie, B. J.; Holaday, C. R.; Nguyen, T.; Hergenrother, P. J. "Phenylcinnamides as Novel Antimitotic Agents" J. Med. Chem. 2010, 53, 3964-3972.

Bair, J. S.; Palchaudhuri, R.; Hergenrother, P. J. "Chemistry and Biology of Deoxynyboquinone, a Potent Inducer of Cancer Cell Death" J. Am. Chem. Soc.2010, 132, 5469-5478.

Peterson, Q. P.; Goode, D. R.; West, D. C.; Botham, R. C.; Hergenrother, P. J. "Preparation of the Caspase-3/-7 Substrate Ac-DEVD-pNA via Solution-Phase Peptide Synthesis" Nature Protocols 2010, 5, 294-302.

Peterson, Q.P.; Hsu, D.C.; Goode, D.R.; Novotny, C.J.; Totten, R.K.; Hergenrother, P.J. "Procaspase-3 Activation as an Anti-Cancer Strategy: Structure-Activity Relationship of PAC-1, and its Cellular Co-Localization with Caspase-3" J. Med. Chem. 2009, 52, 5721-5731.

Meyer, S.T.; Hergenrother, P.J. "Small Molecule Ligands for Bulged RNA Secondary Structures" Org. Lett. 2009, 11, 4052-4055.

Peterson, Q.P.; Goode, D.R.; West, D.C.; Ramsey, K.N.; Lee, J.J.Y.; Hergenrother, P.J. "PAC-1 Activates Procaspase-3 in vitro Through Relief of Zinc-Mediated Inhibition" J. Mol. Biol. 2009, 388, 144-158.

Thompson, C.M.; Quinn, C.A.; Hergenrother, P.J. "The Total Synthesis and Cytoprotective Properties of Dykellic Acid" J. Med. Chem. 2009, 52, 117-125.

Palchaudhuri, R.; Hergenrother, P. J. "Structure-Activity-Relationship of Triphenylmethylamides, Compounds that Potently Induce Apoptosis in Melanoma Cell Lines" Bioorg. Med. Chem. Lett. 2008, 18, 5888-5891.

Williams, J. J.; Hergenrother, P. J. "Exposing Plasmids as the Achilles' Heel of Drug-Resistant Bacteria" Curr. Opin. Chem. Biol. 2008, 12, 389-399.

Palchaudhuri, R.; Nesterenko, V.; Hergenrother, P. J. "The Complex Role of the Triphenylmethyl Motif in Anti-Cancer Compounds" J. Am. Chem. Soc. 2008, 130, 10274-10274.

Chan, L. C.; Pineda, M.; Heeres, J. T.; Hergenrother, P. J., Cunningham, B. T. “A General Method for Discovering Inhibitors of Protein-DNA Interactions Using Photonic Crystal Biosensors” ACS Chem. Biol. 2008, 3, 437-448.

Palchaudhuri, R.; Nesterenko, V.; Hergenrother, P. J. “The Complex Role of the Triphenylmethyl Motif in Anti-Cancer Compounds” J. Am. Chem. Soc. 2008, 130, 10274-10281.

Leslie, B. J.; Hergenrother, P. J. “Identification of the cellular targets of bioactive small organic molecules using affinity reagents” Chem. Soc. Rev. 2008, 37, 1347-1360 (review).

Goode, D. R.; Totten, R. K.; Heeres, J. T.; Hergenrother, P. J. “Identification of Promiscuous Small Molecule Activators in High-Throughput Enzyme Activation Screens” J. Med. Chem. 2008, 51, 2346-2349.

Thomas, J. R.; Hergenrother, P. J. “Targeting RNA with Small Molecules” Chem. Rev. 2008, 108, 1171-1224 (review).

Musk, D. J.; Hergenrother, P. J. “Chelated Iron Sources are Inhibitors of Psudomonas aeruginosa Biofilms and Distribute Efficiently in an in vitro Model of Drug Delivery to the Human Lung” J. Applied Microbiol. 2008, 105, 380-388.

Wang, N. R.; Hergenrother, P. J. "A Continuous Fluorometric Assay for the Assessment of MazF Ribonuclease Activity" Anal. Biochem. 2007, 371, 173-183.

Nottbohm, A. C.; Dothager, R. S.; Putt, K. S.; Hoyt, M. T.; Hergenrother, P. J. "A Novel Colorimetric Substrate for Poly (ADP-Ribose) Polymerase-1, VPARP, and Tankyrase-1" Angew. Chem. Int. Ed. 2007, 46, 2066-2069.

Sienkiewicz, P.; Ciolino, H.; Leslie, B. J.; Hergenrother, P. J.; Singletary, K.; Yeh, G. C. "A Novel Synthetic Analogue of a Constituent of Isodon excisus Inhibits Transcription of CYP1A1, -1A2, and -1B1 by Preventing Activation of the Aryl Hydrocarbon Receptor" Carcinogenesis, 2007, 28, 1052-1057.

Moritz, E. M.; Hergenrother, P. J. "Toxin-Antitoxin System are Ubiquitous and Plasmid-Encoded in Vancomycin-Resistant Enterococci" Proc. Natl. Acad. Sci. 2007, 104, 311-316.



Vanquish Oncology announces a multimillion dollar investment to move PAC-1 to clinical trials for human cancer patients. Read the article here.

On January 7, 2013 StemPar Sciences, Inc. (South San Francisco) announced the licensing of the DNQ family of anticancer compounds developed in the Hergenrother lab. Read the article here.

C&E News highlight of Hergenrother lab method to synthesize complex and diverse compounds from natural products. Read the C&E News article here.

Vanquich Oncology, Inc. founded to develop procaspase-3 activating compounds from the Hergenrother Lab. For more information, click here.

A compound discovered in the Hergenrother lab shows promise in a small Phase 1 clinical trial in pet dogs with lymphoma. Read more at the UIUC News Bureau

Peterson, Q.P.; Hsu, D.C.;Novotny, C.J.; West, D.C.;Kim, D.;Schmit, J.M.; Dirikolu, L.;Hergenrother, P.J.; Fan, T.M. &quotDiscovery and Canine Preclinical Assessment of a Nontoxic Procaspase-3 Activating Compound&quot Cancer Res. 2010,70,7232-7241.

Doctors in the UIUC School of Veterinary Medicine are enrolling dogs with cancer for a Phase I Clinical Trial with one of the anti-cancer compounds discovered in the Hergenrother laboratory.

Chan, L. C.; Pineda, M.; Heeres, J. T.; Hergenrother, P. J., Cunningham, B. T. "A General Method for Discovering Inhibitors of Protein-DNA Interactions Using Photonic Crystal Biosensors" ACS Chem. Biol. 2008, 3, 437-448.

On July 23, 2007 BioLineRx announced the licensing of an anti-cancer agent developed in the Hergenrother laboratories.

Putt, K. S.; Chen, G. W.; Pearson, J. M.; Sandhorst, J. S.; Hoagland, M. S.; Kwon, J.-T.; Hwang, S.-K.; Jin, H.; Churchwell, M. I.; Cho, M.-H.; Doerge, D. R.; Helferich, W. G.; Hergenrother, P. J. "Small-Molecule Activation of Procaspase-3 to Caspase-3 as a Personalized Anticancer Strategy" Nature Chemical Biology 2006, 2, 543-50.

Musk, D.J.; Banko, D.A.; Hergenrother, P.J. "Iron Salts Perturb Biofilm Formation and Disrupt Existing Biofilms of Pseudomonas aeruginosa." Chem. Biol., 2005, 12, 789-796.

Dothager, R.S.; Putt, K.S.; Allen, B.J.; Leslie, B.J.; Nesterenko, V.; Hergenrother, P.J. "Synthesis and Identification of Small Molecules that Potently Induce Apoptosis in Melanoma Cell Through G1 Cell Cycle Arrest." J. Am. Chem. Soc., 2005, 127, 8686-8696.
Chemical & Engineering News Highlight

DeNap, J. B.; Thomas, J. R.; Musk, D. J.; Hergenrother, P. J. "Combating Drug-Resistant Bacteria: Small Molecule Mimics of Plasmid Incompatibility as Antiplasmid Compounds" J. Am. Chem. Soc. 2004, 126, 15402-15404.


Hergenrother, P. J.; Putt, K. S.; Peterson, Q. P.; Fako, V. “Compositions and Methods Including Cell Death Inducers and Procaspase Activation”  issued on November 26, 2013 as U.S. patent 8,592,584.

Hergenrother, P. J.; Nesterenko, V.; Putt, K. S.; Palchaudhuri, R. “Phosphorous-Containing Compounds Including Triphenylmethylphosphonate Esters for the Treatment of Melanoma and Other Cancers” issued on May 4, 2010 as U.S. patent 7,709,465.

Hergenrother, P. J.; Nesterenko, V.; Putt, K. S.; Allen, B. J.; Leslie, B.; Dothager, R. “Compounds and Methods for Treatment of Cancer and Modulation of Programmed Cell Death for Melanoma and Other Cancer Cells” issued Dec. 15, 2009 as U.S. Patent 7,632,972.

Schreiber, S. L.; MacBeath, G.; Koehler, A. K.; Hergenrother, P. J.; Depew, K. M. "Small Molecule Printing"  issued Nov. 30, 2004 as U.S. Patent 6,824,987.

Photo of Paul J. Hergenrother