Faculty

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Our work centers on two nascent technologies that not only borrow from the structure of nature’s bioactive molecules but also from nature's approaches to synthesize molecules and assess them for function. The application of these technologies is focused on advances in medicinal chemistry.

DNA-ecoded chemical libraries. In the first area, we build synthetic small molecule libraries that are covalently linked encoding DNA scaffolds. Within the past few years, DNA-encoded chemical libraries (DELs) have been adopted at every major pharmaceutical company for hit generation and lead discovery. Several successful cases have been reported yielding multiple clinical candidates. The DEL approach has the ability to generate and assay small molecule libraries of much greater complexity than by any other approach. Rather than screening molecules in discrete assays, DELs can be assessed collectivly for binding to a protein target by a selection assay, all together, in a single tube. The cost, effort, and infrastructure required are reduced dramatically, particularly in comparison to traditional high-throughput screening (HTS). This approach enables medicinal chemistry to capitalize on many of the amazing capabilities of molecular biology, such has high detection sensitivity via DNA amplification (PCR) and massively parallel analysis of DNAs in next-generation DNA sequencing. Our work in this area involves development of novel libraries and selection strategies for discovery of protein-protein interaction inhibitors that are mediated by short linear peptide motifs, with a particular focus on protein kinases and chromodomains. We are using these newly developed approaches to develop therapeutic lead molecules for application in treating cancer, Alzheimer's disease, and malaria.

DNA-linked probes for protein assays conducted via DNA analysis. In the second area, we have developed an evolution-inspired assay approach to detect sample stimuli using DNA-linked molecules as activity probes.  We have developed DNA-encoded probes for detection of several enzymatic activities, as well as synthetic ligand binding, which allow activity detection through DNA sequence analysis. We work to apply this approach in proteomic activity profiling and in screening of small molecules for enzyme inhibition. Developments in genetic analysis technologies, particularly DNA sequencing, have been transformative to biomedical research. In contrast to genomic information, the barrier to accessing proteomic information, particularly enzyme activity, is dramatically higher. As aberrant enzyme activities are consistently observed in disease, this information is critical for appropriate diagnosis and treatment. As with DNA-encoded libraries, these approaches allow protein assays to harness the power of DNA analysis technologies. Current efforts are focused on developing robust assays for protein targets directly in cell lysates for small molecule screening and in using libraries of protein kinase substrates to understand resistance mechanisms in drug-resistant cancer.

MCMP 690 Exploring the Primary Literature: Medicinal Chemistry and Chemical Biology Section

MCMP 208 Biochemistry for Pharmaceutical Sciences I

Cai, B., El Daibani, A., Che, T., Krusemark, C. J., “Direct Selection of DNA-encoded Libraries for Biased Agonists of Opioid Receptors on Live Cells.” JACS Au. 2023, 3, 4, 1076-1088.

Cai, B., Mhete, A. B., Krusemark, C. J., "Selection Methods for Proximity-dependent Enrichment of Ligands from DNA-encoded Chemical Libraries using Enzymatic Fusion Proteins." Chemical Science. 2023, 14, 245-250.

Wang, S., Hadisurya, M., Tao, W. A., Dykuizen, E. C., Krusemark, C. J., "Covalent Protein Inhibitors via Tyrosine Conjugation with Cyclic Imine Mannich Electrophiles." ChemRxiv. 2022.

Cai, B., Krusemark, C. J., "Multiplexed Small-Molecule Ligand Binding Assays by Affinity Labeling and DNA Sequence Analysis." Angewandte Chemie Int. Ed., 2022, 61, e202113515.

Wang, S., Alpsoy, A., Sood, S., Ordonez-Rubiano, S. C., Dhiman, A., Sun, Y., Jiao, G., Krusemark, C., J., Dykhuizen, E. C., "A Potent, Selective CBX2 Chromodomain Ligand and Its Cellular Activity During Prostate Cancer Neuroendocrine Differentiation." ChemBioChem, 2021, 22(13), 2335-2344. 

Wang, S., Denton, K. D., Hobbs, K. F., Weaver, T., McFarland, J. M. B., Connelly, K. E., Gignac, M. C., Milosevich, N., Hof, F., Paci, I., Musselman, C. A., Dykhuizen, E. C., Krusemark, C. J., “Optimization of Ligands using Focused DNA-encoded Libraries to Develop a Selective, Cell-permeable CBX8 Chromodomain Inhibitor.” ACS Chem. Biol. 2020, 15, 112-131. 

Cai, B., Kim, D., Akhand, S., Sun, Y., Cassell, R., Alpsoy, A., Dykhuizen, E. C., Van Rijn, R. M., Wendt, M. K., Krusemark, C. J., "Selection of DNA-encoded Libraries to Protein Targets Within and On Living Cells." J. Am. Chem. Soc. 2019, 141, 17057-17061.

Kim, D., Sun, Y., Xie, D., Denton, K. E., Chen, H., Lin, H., Wendt, M. K., Post, C. B., Krusemark, C. J., "Application of a Substrate-Mediated Selection with c-Src Tyrosine Kinase to a DNA-encoded Chemical Library." Molecules. 2019, 24(15), 2764

Shinde, A., Hardy, S. D., Kim, D., Akhand, S. S., Jolly, M. K., Wang, W. H., Anderson, J. C., Khodadadi, R. B., Brown, W. S., George, J. T., Liu, S., Wan, J., Levine, H., Willey, C. D., Krusemark, C. J., Geahlen, R. L., Wendt, M. K., "Spleen Tyrosine Kinase-Mediated Autophagy is Required for Epithelial-Mesenchymal Plasticity and Metastasis in Breast Cancer." Cancer Research. 2019, 79(8), 1831-1843

Denton, K. E., Wang, S., Gignac, M. C., Milosevich, N., Hof, F., Dykhuizen, E. C., Krusemark, C. J., "Robustness of In Vitro Selection Assays of DNA-encoded Peptidomimetic Ligands to CBX7 and CBX8." SLAS Discovery, 2018, 23, 417-428.

Kim, D., Jetson, R. R., Krusemark, C. J., "A DNA-assisted Immunoassay for Enzyme Activity via a DNA-linked, Activity-based Probe." Chem. Comm. 2017, 53, 9474-9477.

Denton, K. E., Krusemark, C. J., "Crosslinking of DNA-linked ligands to target proteins for enrichment from DNA-encoded libraries." Med. Chem. Comm. 2016, 7, 2020-2027.

Jetson, R. R., Krusemark, C. J. "Sensing Enzymatic Activity by Exposure and Selection of DNA-encoded Probes." Angewandte Chemie Int. Ed. 2016, 55, 9562-9566.