Ph.D., University of Washington, 2007
Welcome to the Lampe lab! Here, we are interested in making exciting new scientific discoveries that will impact human health in tangible ways. To accomplish this, we combine powerful tools from both biophysical and computational chemistry to understand structure-function relationships in protein drug targets and to design new chemical entities to modulate these targets. Currently, there are two major research initiatives in our lab:
Determining the mechanism of ligand binding and translocation in organic cationic drug transporters
The human organic cation transporter 1 (OCT1), an important polyspecific transporter of the SLC22 class, is involved in the uptake and transport of a wide variety of cationic drugs and endogenous compounds. It is primarily expressed in the liver, but significant amounts are also found in the heart, brain, and placenta. Recent work has demonstrated that polymorphisms in this transporter can greatly diminish the efficacy of certain drugs, including the antidiabetic agent metformin and the antineoplastic agent imatinib. Despite its important role in drug disposition and efficacy, little is known regarding the molecular details of ligand binding and transport in OCT1. Understanding the structural and functional characteristics of OCT1, including the basis for substrate and inhibitor selectivity, will greatly improve opportunities for cationic drug discovery and design. To this end, we employ novel nuclear magnetic resonance (NMR) techniques using the site-specific incorporation of 13C and 15N labeled unnatural amino acids in heterologously expressed OCT1 to directly map the binding sites of substrate and inhibitor ligands and examine the dynamics of the protein during the ligand translocation process. Data obtained from these NMR investigations will be incorporated into a computational model of OCT1 in order to perform long-timescale (~1 µsec) molecular dynamics simulations of the OCT1 protein. In turn, the results from these simulations will provide us with an accurate model of the ligand translocation process. Armed with this model, we will be able to predict a priori which ligands will act as substrates, inhibitors, or transactivators of OCT1. Ultimately, this knowledge will lead to the development of safer and more effective medicines with less risk for drug-drug interactions.
Designing novel bivalent inhibitors to target the anti-apoptotic protein Survivin
Survivin is an important protein involved in apoptosis, cell proliferation, and angiogenesis. Additionally, its expression is upregulated in almost all types of cancer. Downregulation of survivin expression or inactivation of its function has been shown to inhibit tumor growth and increase survival rates in numerous animal models. The survivin protein is an important member of the chromosomal passenger complex, which is essential to chromosomal segregation and mitotic spindle formation during mitosis. Also a member of the Inhibitor of Apoptosis (IAP) family of proteins, survivin is thought to inhibit apoptosis in cancerous cells by interacting with the SMAC/DIABLO complex and/or by inhibiting cellular caspase activity, although the molecular details of these processes remain unclear. Recently, two distinct small molecule binding sites on the surface of the protein have been identified through Structure-Activity-Relationship screening by NMR (SAR-by-NMR). Attempts to target the sites individually have not led to substantial survivin inhibition in vivo, despite success with this approach in vitro. Therefore, we are currently designing novel bivalent inhibitors that target both sites simultaneously to optimally harness the cooperative binding energy afforded by such an approach. Initially, a small library of bivalent inhibitors will be screened against survivin using SAR-by-NMR to identify lead compounds. Lead compound candidates will be further developed to improve affinity and specificity using standard medicinal chemistry techniques and prospective drug candidates will be tested using in vitro cell culture and in vivo mouse model systems. Targeting survivin using bivalent inhibitors is likely to be a fruitful approach to treat currently intractable cancers.
If you are interested in joining us as a graduate student or a post-doctoral scholar on this exciting voyage of scientific discovery, please contact Dr. Lampe via e-mail at: firstname.lastname@example.org. We look forward to hearing from you!
Lampe, J. N., Brandman, R., Sivaramakrishnan, S., and Ortiz de Montellano, P. R. (2010). Two-dimensional NMR and all-atom molecular dynamics of cytochrome P450 CYP119 reveal hidden conformational substates. J. Biol. Chem. 285, 9594-9603.
Lampe, J. N., Floor, S. N., Gross, J. D., Nishida, C. R., Jiang, Y., Trnka, M. J., and Ortiz de Montellano, P. R. (2008). Ligand-induced conformational heterogeneity of cytochrome P450 CYP119 identified by 2D NMR spectroscopy with the unnatural amino acid 13C-p -methoxyphenylalanine. J. Am. Chem. Soc., 130, 16168-16169.
Nath, A., Fernandez, C., Lampe, J. N., and Atkins, W. M. (2008). Spectral resolution of a second binding site for Nile Red on cytochrome P4503A4. Arch. Biochem. Biophys. 474, 198-204.
Lampe, J. N., Fernandez, C., Nath, A., and Atkins, W. M. (2007). Nile Red is a fluorescent allosteric substrate of cytochrome P450 3A4. Biochemistry 47, 509-516.
Wen, B., Lampe, J. N., Roberts, A. G., Atkins, W. M., David Rodrigues, A., and Nelson, S. D. (2006). Cysteine 98 in CYP3A4 contributes to conformational integrity required for P450 interaction with CYP reductase. Arch. Biochem. Biophys. 454, 42-54.
Roberts, A. G., Diaz, M. D., Lampe, J. N., Shireman, L. M., Grinstead, J. S., Dabrowski, M. J., Pearson, J. T., Bowman, M. K., Atkins, W. M., and Campbell, A. P. (2006). NMR studies of ligand binding to P450(eryF) provides insight into the mechanism of cooperativity. Biochemistry 45, 1673-1684.
Lampe, J. N., and Atkins, W. M. (2006). Time-resolved fluorescence studies of heterotropic ligand binding to cytochrome P450 3A4. Biochemistry 45, 12204-12215.
Wen, B., Doneanu, C. E., Lampe, J. N., Roberts, A. G., Atkins, W. M., and Nelson, S. D. (2005). Probing the CYP3A4 active site by cysteine scanning mutagenesis and photoaffinity labeling. Arch. Biochem. Biophys. 444, 100-111.
Compagno, D., Lampe, J. N., Bourget, C., Kutyavin, I. V., Yurchenko, L., Lukhtanov, E. A., Gorn, V. V., Gamper, H. B., Jr., and Toulme, J. J. (1999). Antisense oligonucleotides containing modified bases inhibit in vitro translation of Leishmania amazonensis mRNAs by invading the mini-exon hairpin. J. Biol. Chem. 274, 8191-8198.
Jed N Lampe, PhD
4069 HLSIC; MS-1018
3901 Rainbow Blvd.
Kansas City, Kansas 66160
F: (913) 588-7501