Research

Research in the Harki laboratory focuses on the design, synthesis and biophysical characterization of novel small molecules that influence cellular function.  Applications for these molecules range from anticancer drug discovery to new tools for modern biotechnology research.  Our core science is organic chemistry. However, we use techniques of modern molecular biology, genetics, and genomics to probe the biological activities of the compounds we synthesize.


Small Molecule APOBEC3 Inhibitors. In collaboration with Professor Reuben Harris and coworkers (University of Minnesota), we are developing first-in-class inhibitors of APOBEC3 DNA cytosine deaminases. Cellular APOBEC3 enzymes participate in the favorable restriction of pathogenic viruses by deaminating foreign DNA cytosines to uracils, resulting in clearance of the targeted DNA strand. However, APOBEC3 enzymes can also contribute to the genetic diversity of HIV-1 (APOBEC3G) and cancer genomes (APOBEC3B). Therefore, APOBEC3 enzyme inhibitors are important tool compounds for studying APOBEC3 biochemistry and may yield innovative new therapeutics for HIV-1 and cancer.  Our team has reported the first-in-class inhibitors of APOBEC3G, MN30 (ACS Chem. Biol. 2012) and MN256 (ChemMedChem 2013). These molecules were discovered by combining high-throughout screening with iterative rounds of subsequent chemical synthesis (structural optimization of analogue) and biochemical assays (characterization of analogue). Additional inhibitors are under development in our laboratories, including the first-in-class inhibitor of the cancer-associated enzyme, APOBEC3B.


 

Anticancer Natural Products & Analogues. We are performing structure-activity relationship studies and elucidating the molecular targets of two sesquiterpene lactone (SL) natural products, helenalin and parthenolide. Both compounds are micromolar inhibitors of the pro-inflammatory transcription factor NF-κB. Helenalin is considered by some researchers to be a selective inhibitor of NF-κB p65, which is uncommon for SL natural products and covalent molecules in general. Using synthesized probes, we are studying the proteome reactivity properties of helenalin. The related SL natural product parthenolide is known to eradicate acute myelogenous leukemia (AML) stem cells with little toxicity to healthy hematopoietic stem cells. Using  synthesized probes, we are characterizing the molecular targets of parthenolide in primary AML cells to explain this remarkable selectivity. We hypothesize that elucidating the molecular targets of parthenolide will reveal new strategies for inhibiting AML stem cells. Our group is also developing novel analogues based on helenalin and parthenolide for applications as cancer therapeutics.

In related studies with Professor Andrew Harned and coworkers (University of Minnesota), we have characterized the NF-κB inhibitory activities of structurally simplified cryptocaryone analogues (ACS Med. Chem. Lett. 2012). Additionally, in collaboration with Professor Kay Brummond and coworkers (University of Pittsburgh), we have elucidated the NF-κB and cancer cell inhibitory activities of fully synthetic guaianolide analogues, which mimic that class of natural products (Org. Lett. 2013).


Other projects currently underway in the Harki laboratory:

-Development of light-regulated nucleosides, nucleotides, and nucleic acids as chemical probes of biological function. These reagents are being developed to control gene expression in cells.


Requests for samples of chemical probes should be sent to Professor Harki.