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Daniel Flaherty

Daniel Flaherty Profile Picture

Assistant Professor
Ph.D., University of Nebraska Medical Center, 2010

Contact Info:

Training Group(s):
Immunology and Infectious Diseases
Chemical Biology

Current Research Interests:

Resistance to commonly prescribed antibiotics is becoming an increasingly dangerous threat to society.  Several strains of pathogenic bacteria have displayed resistance toward drugs that are commonly used as a last line of defense for treatment of these infections.  Therefore, there is an urgent need to not only expand upon currently known antimicrobial chemical space but to also validate novel therapeutic targets for treatment of these infections.  To this end the Flaherty lab utilizes a combination of traditional high-throughput screening techniques and contemporary fragment-based drug discovery practices to identify and optimize new chemical scaffolds for inhibition of novel antimicrobial targets.  These techniques are combined with thermodynamic characterization of the ligand-protein binding event to gain a more intimate knowledge of the processes involved in the binding event.  We then utilize this information to optimize inhibitors not only for increased potency but also for increased selectivity while maintaining optimal physicochemical properties of the molecule.  The lab then uses these novel inhibitors to validate these enzymes as viable antibiotic therapeutic targets.

One area of research that our lab is interested in is developing potent and selective inhibitors versus bacterial RNA degradation targets.  RNA degradation is an essential cellular process for viability in all organisms.  Bacterial RNA degradation pathways differ significantly from human pathways making targeting RNA degradation an attractive antimicrobial strategy. RNase E is highly conserved across all Gram-negative pathogenic species and catalyzes two essential steps in the mRNA degradation/tRNA maturation pathway.  Furthermore, research has shown that knockout of this enzyme can lead to inhibition of two essential cellular processes resulting in a lower potential for resistance.  However, there are no reported inhibitors for RNase E. Therefore, the Flaherty lab has embarked in a multidisciplinary effort to identify and optimize RNase E inhibitors utilizing a bi-lateral traditional HTS and FBDD approach coupled with structure-based drug design to arrive at novel and potent inhibitors. Furthermore, the use of thermodynamics to dissect the attributes that correlate with compound affinity provides a clearer picture of what drives binding.  Finally, ligand-bound structural determination provides key information for structure-based design of inhibitors. Such inhibitors will be instrumental for in vivo validation of RNase E as a viable, broad-spectrum Gram-negative therapeutic target.

While RNase E is essential for RNA degradation/maturation in all Gram-negative species, the enzyme RnpA is responsible for these processes in Gram-positive pathogens.  RnpA is a small protein that has been shown to be an integral part of at least two RNA processing enzymatic complexes.  Recent research has shown that inhibition of RnpA has a significant effect on both mRNA degradation and tRNA maturation.  RnpA is also conserved across several Gram-positive species and represents a promising Gram-positive antimicrobial target.  Utilizing the same strategy we have identified novel S. aureus RnpA inhibitors.  Currently our laborotary is utilizing structural information and computational models to map where these inhibitors bind on the protein.  Furthermore, we are working to elucidate the role different binding sites on RnpA play in each essential process.  These inhibitors will prove essential for validating RnpA as a viable Gram-positive therapeutic target.

A third project the Flaherty lab is currently pursuing is the development of potent and selective inhibitors for the human deubiquitinase UCHL1.  The UCH family of enzymes has been implicated to play key roles in cancers of various tissues.  Recently UCHL1 was even shown to be integral in deubiquitinating hypoxia-inducible factor 1a leading to metastasis.  Currently there are two small molecule inhibitors for UCHL1, however these inhibitors significantly lack potency and selectivity versus other UCHs such as UCHL3 and UCHL5.  Therefore, there is urgent need to develop a potent and selective inhibitor that can serve as a valuable tool to further elucidate UCHL1’s role in cancer biology and metastasis and validate UCHL1 inhibition as a viable anticancer strategy.  Our lab collaborates with the laboratory of Dr. Chittaranjan Das in the Department of Chemistry at Purdue University to identify and develop best-in-class small molecule inhibitors versus UCHL1.  The Das lab has solved the UCHL1 crystal structure and is a leader in UCHL1 biochemistry; thus, this collaboration provides an exciting opportunity to be at the forefront of the UCHL1 field.

For more information please visit the laboratories webpage:

Selected Publications:

Perlmutter J. I.; Forbes, L. T.; Krysan, D. J.; Ebsworth-Mojica, E.; Dunman, P. M.; Flaherty, D. P.* Repurposing the antihistamine terfenadine for antimicrobial activity against Staphylococcus aureus. J. Med. Chem. 2014, 57, 8540 – 8562.

Flaherty, D. P; Miller, J. R.; Garshott, D. M.; Hedrock, M.; Gosalia, P.; Li, Y.; Milewski, M.; Sugarman, E.; Suyama, E.; Nguyen, K.; Vasile, S.; Salaniwal, S.; Stonich, D.; Su, Y.; Vicchiarelli, M.; Chung, T. D. Y.; Pinkerton, A. B.; Aubé, J.; Callaghan, M. U.; Golden, J. E.; Fribley, A. M.; Kaufman, R. J. Discovery and development of selective activators targeting the apoptotic CHOP pathway of the unfolded protein response. ACS Med. Chem. Lett. 2014, 5, 1278 – 1283.

Matharu, D. S.; Flaherty, D. P.; Simpson, D. S; Chung, D.; Yan, D.; Noah, J. W.; Jonsson, C. B.; White, E. L.; Aubé, J.; Plemper, R. K.; Severson, W. E.; Golden, J. E.  Optimization of potent and selective quinazolinediones: inhibitors of respiratory syncytial virus that block RNA-dependent-RNA-polymerase complex activity. J. Med. Chem. 2014, 57, 10314 – 10328.

Flaherty, D. P.; Simpson, D. S.; Miller, M.; Maki, B. E.; Zou, B.; Shi, J.; Wu, M.; McManus, O. B.; Aubé, J.; Li, M.; Golden, J. E. Potent and Selective Inhibitors of the TASK-1 Potassium Channel through Chemical Optimization of a Bis-Amide Scaffold. Bioorganic and Medicinal Chemistry Letters, 2014, 24, 3968 – 3973.

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