Chemical Biology

Synthetic compounds designed to potently and selectively interact with specific biomolecules have served as powerful tools for establishing biological function, and for many biomolecular targets, have resulted in important, life-saving therapeutic agents. The Ellman lab has continually sought to leverage synthetic chemistry to address important biomedical problems. In fact, the design, high throughput/combinatorial synthesis, and testing of drug-like small molecules was the first set of projects to be carried out by the Ellman group, including demonstrating this approach for the first time for nonpolymeric molecules as implemented for the privileged benzodiazepine framework as well as early examples of library design using structure-based docking of virtual libraries with Tack Kuntz (UCSF).

Enzymes are proteins that catalyze a majority of the chemical transformations required by living organisms and as such they play central roles in virtually all biological processes. Enzyme inhibition also provides a powerful approach for the treatment of disease. In collaboration with Charly Craik (UCSF), the Ellman lab developed positional scanning protease substrate profiling methods to rapidly determine preferred cleavage sequences for proteases, enzymes that hydrolyze amide bonds in peptides and proteins. This information can facilitate the identification of natural protease substrates to establish their biological roles and can aid in the design of potent and selective inhibitors. The methods developed with Craik have now been applied to hundreds of proteases by numerous academic and industrial labs.

Due to the rapidity and reliability by which substrate cleavage efficiency can be obtained, the Ellman lab developed a substrate-based fragment identification and optimization approach for small molecule enzyme inhibitor discovery. We first developed the approach as a platform for protease inhibitor discovery and applied it to the identification of potent and selective inhibitors to a number of therapeutically relevant proteases. For example, the Ellman group used the approach to develop highly potent and selective inhibitors of cathepsin S such as 1 (Figure 1A), which is implicated in autoimmune disorders and cancer.  Indeed, due to the potency and selectivity of inhibitor 1, it served as the starting point for further drug development by Boehringer Ingelheim, and in collaboration with Matt Bogyo at Stanford, provided the key binding motif for near-infrared activity-based-probes for imaging cathepsin S activity in vivo. Potent, selective and orally available inhibitors such as have also been developed against cruzain (Figure 1B), which is an essential protease of Trypanosoma cruzi and is the causative agent of Chagas’ disease. The McKerrow lab at UCSF determined that inhibitor eliminated all symptoms of disease in infected mice and produced a parasitological cure in a significant percentage of the animals. We have also developed the substrate-based fragment approach for the discovery of small molecule inhibitors to other enzyme classes, including protein tyrosine phosphatases and protein arginine deiminases.

Figure 1. Potent and selective protease inhibitors identified by substrate-based fragment identification and optimization

The depth and breadth of cutting edge research at Yale School of Medicine provides many exciting opportunities for collaboration. As one example, we collaborated with Angus Nairn and Paul Lombroso along with researchers at AZN to identify nanomolar, selective inhibitors of striatal enriched protein tyrosine phosphatase, implicated in neurological disorders, including Alzheimer’s disease (Figure 2). We have also collaborated with Ya Ha (Yale Pharmacology) on the structure-based development of potent and selective lipid kinase inhibitors implicated in cancer and separately with Anton Bennett, Elias Lolis and Karen Anderson (Yale Pharmacology) on the structure-based development of selective allosteric inhibitors of MKP5, a protein tyrosine phosphatase implicated in diseases such as muscular dystrophy.

Figure 2X-ray crystal structures of striatal enriched protein tyrosine phosphatase inhibitors

Relevant Publications

Chen, S.; Chandra Tjin, C.; Gao, X.; Xue, Y.; Jiao, H.; Zhang, R.; Wu, M.; He, Z.; Ellman, J. A.; Ha, Y.
Pharmacological inhibition of PI5P4Kα/β disrupts cell energy metabolism and selectively kills p53-null tumor cells
Proc. Natl. Acad. Sci. USA  2021118, e2002486118.  
Gannam, Z. T. K.; Min, K.; Shillingford, S. R.; Zhang, L.; Herrington, J.; Abriola, L.; Gareiss, P. C.; Pantouris, G.; Tzouvelekis, A.; et al.
An allosteric site on MKP5 reveals a strategy for small molecule inhibition
Science Signaling  202013, eaba3043.  
Scamp, R. J.; deRamon, E.; Paulson, E. K.; Miller, S. J.; Ellman, J. A.
Co(III)-Catalyzed C-H Amidation of Dehydroalanine for the Site-Selective Structural Diversification of Thiostrepton
Angew. Chem. Int. Ed.  202059, 890-895.  
Chandra Tjin, C.; Wissner, R.; Jamali, H.; Schepartz, A.; Ellman, J. A.
Synthesis and Biological Evaluation of an Indazole-Based Selective Protein Arginine Deiminase 4 (PAD4) Inhibitor
ACS Med. Chem. Lett.  20189, 1013–1018.  
Xu, J.; Hartley, B. J.; Kurup, P.; Phillips, A.; Topol, A.; Xu, M.; Ononenyi, C.; Foscue, E.; Ho, S. M.; Baguley, T. D.; Carty, N.; Barros, C. S.; Müller, U.; Gupta, S.; Gochman, P.; Rapoport, J.; Ellman, J. A.; et al.
Inhibition of STEP61 Ameliorates Deficits in Mouse and hiPSC-Based Schizophrenia Models
Mol. Psychiatry  201823, 271–281.  
Tjin, C. C.; Otley, K. D.; Baguley, T. D.; Kurup, P.; Xu, J.; Nairn, A. C.; Lombroso, P. J.; Ellman, J. A.
Glutathione-Responsive Selenosulfide Prodrugs as a Platform Strategy for Potent and Selective Mechanism-Based Inhibition of Protein Tyrosine Phosphatases
ACS Cent. Sci.  20173, 1322–1328.  
Witten, M. R.; Wissler, L.; Snow, M.; Geschwindner, S.; Read, J. A.; Brandon, N. J.; Nairn, A. C.; Lombroso, P. J.; Käck, H.; Ellman, J. A.
X-ray Characterization and Structure-Based Optimization of Striatal-Enriched Protein Tyrosine Phosphatase Inhibitors
J. Med. Chem.  201760, 9299–9319.  
Jamali, H.; Khan, H. A.; Tjin, C. C.; Ellman, J. A.
Cellular Activity of New Small Molecule Protein Arginine Deiminase 3 (PAD3) Inhibitors
ACS Med. Chem. Lett.  20167, 847–851.  
Xu, J.; Kurup, P.; Baguley, T.; Foscue, E.; Ellman J. A.; Nairn, A. C.; Lombroso, P. J.
Inhibition of the Tyrosine Phosphatase STEP61 Restores BDNF Expression and Reverses Motor and Cognitive Deficits in Phencyclidine-Treated Mice
Cell. Mol. Life Sci.  201673, 1503-1514.  
Azkona, G.; Saavedra, A.; Aira, Z.; Aluja, D.; Xifró, X.; Baguley, T.; Alberch, J.; Ellman J. A.; Lombroso, P. J.; Azkue, J. J.; Pérez-Navarro, E.
Striatal-Enriched Protein Tyrosine Phosphatase Modulates Nociception: Evidence from Genetic Deletion and Pharmacological Inhibition
Pain  2016157, 377-86.  
Xu, J.; Kurup, P. K.; Azkona, G. M.; Baguley, T. D.; Saavedra, A. C.; Nairn, A. C.; Ellman, J. A.; Perez-Navarro, E.; Lombroso, P. A.
Down-Regulation of BDNF in Cell and Animal Models Increases Striatal-Enriched Protein Tyrosine Phosphatase STEP61 Levels
J. Neurochem.  2016136, 285–294.  
Oresic Bender, K.; Ofori, L.; van der Linden, W. A.; Mock, E. D.; Datta, G.; Chowdhury, S.; Li, H.; Segal, E.; Lopez, M. S.; Ellman, J. A.; Figdor, C. G.; Bogyo, M.; Verdoes, M.
Design of a Highly Selective Quenched Activity-Based Probe and Its Application in Dual Color Imaging Studies of Cathepsin S Activity Localization
J. Am. Chem. Soc.  2015137, 4771–4777.  
Jamali, H.; Khan, H. A.; Stringer, J. A.; Chowdhury, S. Ellman, J. A.
Identification of Multiple Structurally-Distinct, Nonpeptidic Small Molecule Inhibitors of Protein Arginine Deiminase 3 Using a Substrate-Based Fragment Method
J. Am. Chem. Soc.   2015137, 3616–3621.  
Xu, J.; Chatterjee, M.; Baguley, T. D.; Brouillette, J.; Kurup, P.; Ghosh, D.; Kanyo, J.; Zhang, Y.; Seyb, K.; Ononenyi, C.; Foscue, E.;Cuny, G. D.; Glicksman, M. A.; Greengard, P.; Lam, T. T.; Tautz, L.; Nairn, A. C.; Ellman, J. A.; Lombroso, P. A.
Inhibitor of the Tyrosine Phosphatase STEP Reverses Cognitive Deficits in a Mouse Model of Alzheimer’s Disease
PLoS Biol.  201412, e1001923.  
Baguley, T. D.; Xu, H.-C.; Chatterjee, M.; Nairn, A. C.; Lombroso, P. J.; Ellman, J. A.
Substrate-Based Fragment Identification for the Development of Selective, Nonpeptidic Inhibitors of Striatal-Enriched Protein Tyrosine Phophatase
J. Med. Chem.  201356, 7636-7650.