Dehua Pei obtained his B.S. Degree in Chemistry from Wuhan University, China in 1986 and his Ph.D. Degree in organic chemistry from University of California, Berkeley in 1991, working under the direction of Peter G. Schultz. After a postdoctoral stint with Christopher T. Walsh at Harvard Medical School, he joined the faculty at OSU in 1995 as an Assistant Professor of Chemistry. He was promoted to Associate Professor in 2001 and to Professor in 2004. 

We are conducting two types of research at the interface of chemistry and biology. In the first area (chemical biology), we develop new chemical methods/probes and apply them to determine the molecular mechanisms of biological processes (e.g., eukaryotic cell signaling). In the second area (medicinal chemistry), we develop new methodologies to synthesize and screen large combinatorial libraries of macrocyclic compounds against proteins and other macromolecules involved in human diseases (e.g., cancer) to identify potential therapeutic agents. The following projects are under current investigation in our group.

1. Discovery of New Protein-Protein Interactions. Protein-protein interaction forms the basis of essentially all cellular processes. Many of the interactions are mediated by >2000 modular domains, which recognize short peptide motifs in their partner proteins (e.g., SH2, PTB, BIR, BRCT, BUZ, and PDZ domains). However, for most of these domains, their physiological binding partners and cellular functions are yet unknown. We use a chemical/bioinformatics approach to identify the in vivo binding partners of these domains. First, a modular domain is screened against a peptide library to identify its peptide recognition motif(s). The peptide motif is next used to search the human proteome to identify its potential cellular targets, which are subsequently validated by cell biology and/or proteomics methods. Finally, the specificity information is used to design specific inhibitors to disrupt the protein-protein interaction inside a cell, in order to determine the physiological function of the interaction. In addition, mutations in the protein domains can alter their binding specificity and cause diseases such as cancer. By comparing the specificity differences between the wild-type and disease-causing mutants, we can gain useful insights into the disease mechanism and identify new protein targets for drug design.

2. Identification of Enzyme Substrates. More than 160,000 serine, threonine, and tyrosine residues on >18,000 mammalian proteins are phosphorylated during various cellular events. The proper level of phosphorylation is controlled by the opposing actions of ~500 protein kinases and >100 phosphatases. Identification of the substrate(s) of a kinase or phosphatase has been a challenging task. We are tackling this problem with the chemical/bioinformatics approach noted above. A peptide library is first screened against a kinase or phosphatase of interest to determine its substrate specificity profile. The consensus sequence(s) is then used to search the protein databases to identify its potential protein substrates, which are subsequently validated by cellular techniques. Another goal is to utilize the substrate specificity data to design specific enzyme inhibitors, which will in turn be used as research tools to study the cellular functions of the enzyme and as potential therapeutic agents.

3. Synthesis and Screening of Macrocyclic Compounds. The vast majority of existing drugs are either small molecules (molecular weight <500) or large proteins (molecular weight >5000). Macrocycles (e.g., cyclic peptides) fill in an important gap in the drug structural space (molecular weight = 500-5000) and are especially attractive as inhibitors of protein-protein interactions, which represent an exciting but very challenging class of drug targets for small molecules. We have recently developed a methodology to chemically synthesize and screen large libraries of cyclic peptides. We are now applying this method to develop cyclic peptide inhibitors against enzymes and proteins involved in protein-protein interactions. In addition, we are developing methods to synthesize and screen large libraries of non-peptidic, natural product-like macrocycles.

Major Techniques in Research:

• Solid-phase synthesis of peptide and non-peptidic libraries
• Solution-phase synthesis of library building blocks and other small molecules
• High-throughput library screening and peptide sequencing by mass spectrometry
• Molecular cloning, expression and purification of proteins
• Biophysical characterization of proteins (e.g., fluorescence polarization and surface plasmon resonance)
• Enzyme kinetics and inhibition
• Mammalian tissue culture, co-immunoprecipitation, and western blotting
• Confocal microscopy
• Bioinformatics

Current sources of Research Funding:

• National Institute of General Medical Sciences
• National Cancer Institute

Current Employment of Recent Graduates:

PhD Students: Assistant Professor of Pharmacy, Catholic University of Daegu, South Korea; Scientist, Food and Drug Administration; Scientist, Nestle Research Center, Switzerland; Scientist, Bayer HealthCare; Senior R&D Chemist, Albemarle; Research Chemist, RTI International.

Postdoctoral Associates: Professor of Chemistry, Tsinghua University, China; Professor of Pharmaceutical Chemistry, University of Bonn, Germany; Associate Professor of Chemistry, Wuhan University, China; Associate Professor of Chemistry, China Agricultural University; Chemical Abstracts; Scientist, AstaTech, Inc.

Liu, T., Qian, Z., Xiao, Q., and Pei, D. (2011) High-Throughput Screening of One-Bead-One-Compound Libraries: Identification of Cyclic Peptidyl Inhibitors against Calcineurin/NFAT Interaction. ACS Comb. Sci. 13, 537-546.

Wu, X., Wang, L., Han, Y., Regan, N., Li, P.-K., Villalona-Calero, M., Hu, X., Briesewitz, R., and Pei, D. (2011) Creating Diverse Target-Binding Surfaces on FKBP12: Synthesis and Evaluation of a Rapamycin Analogue Library. ACS Comb. Sci. 13, 486-495.

Zhang, Y., Zhang, J., Yuan, C., Hard, R. L., Park, I.-H., Li, C., Bell, C. E., and Pei, D. (2011) Simultaneous Binding of Two Peptidyl Ligands by a Src Homology 2 Domain. Biochemistry 50, 7637-7646.

Ren, L., Chen, X., Luechapanichkul, R., Selner, N., Meyer, T. M., Wavreille, A.-S., Chan, R., Iorio, C., Zhou, X., Neel, B. G., and Pei, D. (2011) Substrate specificity of protein tyrosine phosphatases 1B, RPTP, SHP-1 and SHP-2. Biochemistry 50, 2339-2356.

Chen, X., Ren, L., Kim, S., Carpino, N., Daniel, J. L., Kunapuli, S. P., Tsygankov, A. Y., and Pei, D. (2010) Determination of the substrate specificity of protein tyrosine phosphatase TULA-2 and identification of Syk as a TULA-2 substrate. J. Biol. Chem. 285, 31268-31276.

Liu, T.; Liu, Y.; Kao, H.-Y.; Pei, D. (2010) Membrane Permeable Cyclic Peptidyl Inhibitors against Human Peptidylprolyl Isomerase Pin1. J. Med. Chem. 53, 2494-2501.

Zhu, J., and Pei, D. (2008) A LuxP-based fluorescent sensor for bacterial autoinducer II. ACS Chem. Biol. 3, 110-119.

Xiao, Q., Zhang, F., Nacev, B. A., Liu, J. O., and Pei, D. (2010) Protein N-terminal processing: Substrate specificity of Escherichia coli and human methionine aminopeptidases. Biochemistry 49, 5588-5599.

Thakkar, A., Cohen, A. S., Connolly, M. D., Zuckermann, R. N., and Pei, D. (2009) High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial Edman degradation and mass spectrometry. J. Comb. Chem. 11, 294−302.

Gopishetty, B., Zhu, J., Rajan, R., Sobczak, A. J., Wnuk, S. F., Bell, C. E., and Pei, D. (2009) Probing the catalytic mechanism of S-ribosylhomocysteinase (LuxS) with catalytic intermediates and substrate analogues, J. Am. Chem. Soc. 131, 1243−1250.

Zhang, Y., Wavreille, A.-S., Kunys, A. R., and Pei, D. (2009) The SH2 domains of inositol polyphosphate 5-phosphatases SHIP1 and SHIP2 have similar specificity but different binding kinetics. Biochemistry 48, 11075-11083.