Daniel Appella, Ph.D. : NIDDK

Daniel Appella, Ph.D.


Education / Previous Training and Experience:
Ph.D., University of Wisconsin - Madison, 1998

Research Statement:

Our research uses synthetic organic chemistry to create new molecules with unique biological activity. Each project that we work on has the potential to evolve into a new strategy for diagnosing or treating a disease. Within our research, we spend most of our time synthesizing molecules, but we also use a large amount of molecular modeling and biophysical techniques to study the molecules we make. We also have several collaborations within the NIH and other institutions to study the biological effects of our molecules in vivo. The following categories summarize the different projects in the group.

Peptide nucleic acids (PNAs) consist of an aminoethylglycine backbone to which nucleobases are attached. These molecules are very flexible, yet they bind to complementary DNA and RNA with high affinity and sequence specificity. There have been numerous biochemical and biomedical applications of PNAs, however there is no general strategy for functionalizing or preorganizing this class of molecules while preserving the binding properties to complementary nucleic acids. Our research is exploring the incorporation of carbocyclic rings and sidechains into the backbone of peptide nucleic acids (PNAs) in order to improve binding to oligonucleotides and provide the basis for design of PNA-based sensors. Proper rigidification of PNAs could significantly enhance their binding properties to DNA and RNA, and improve many of the diagnostic techniques that rely on PNA. Through a combination of molecular modeling techniques, we have found that incorporation of a cyclopentane ring into the ethylenediamine portion of a PNA significantly improves the binding to DNA and RNA. We are currently exploring the generality of this modification in several different PNA sequences. Our future work will place other carbocyclic rings and sidechains into PNAs and we will develop new diagnostic techniques based on our modified PNAs.

In recent years, a wealth of structural information on RNA has emerged. These data have revealed the complexity and diversity of folded structures that RNA can adopt to create protein binding sites or to perform catalytic functions. In many cases, the folded RNA structures approach the complexity of folded protein structures. For several decades, chemists have designed and synthesized organic molecules that bind to the active sites of proteins and inhibit protein functions. The fact that proteins adopt folded, three-dimensional structures with unique binding pockets allows chemists to develop small organic molecules that bind with high affinity and specificity to a target protein. Because RNA can also possess folded, three-dimensional structures, it should be possible for chemists to design new molecules that bind a target RNA with high affinity and specificity. Such molecules could ultimately evolve into new types of drugs that exert their biological effects by targeting RNA. Since the biophysical properties of RNA are very different from proteins, the types of molecules that must be developed for RNA binding will be very different from the molecules that bind to proteins. Currently, RNA is significantly underutilized as a potential target for drug development. Our research aims to design and synthesize organic molecules that can selectively recognize folded RNA structures. In this project, we are examining sidechain-bearing polyamines as molecular scaffolds for the display of RNA binding groups. This strategy will create a new class of molecules that we propose will bind with high affinity and specificity to folded RNAs. We are currently developing syntheses of these polyamines on a solid support, making combinatorial libraries of these molecules, and studying their binding properties to two important RNA targets (TAR RNA and RRE RNA of HIV).

The protein p53 is an important tumor suppressor. When a cell is damaged, p53 is expressed and then cell death (apoptosis) occurs. In order to induce apoptosis, p53 must bind to a specific DNA sequence. Interestingly, approximately 50% of human tumors have mutant p53 protein that is unable to bind its target DNA. If p53 cannot bind DNA, then apoptosis will not occur and a diseased cell will continue to grow and divide. Therefore, developing new methods to restore the normal functions to mutant p53 could lead to new therapies for cancer. Random screenings of combinatorial libraries of organic molecules have identified a few novel molecules that reactivate mutant p53 to bind its DNA target. Inspired by these recent results, we have begun to design our own class of molecules that reactivate mutant p53 in order to probe the unique mechanism that allows small organic molecules to restore normal activity to a mutant protein.

Selected Publications:

1. Englund EA, Appella DH gamma-Substituted Peptide Nucleic Acids Constructed from L-Lysine are a Versatile Scaffold for Multifunctional Display. Angew Chem Int Ed Engl(46): 1414-8, 2007. [Full Text/Abstract]

2. Englund EA, Xu Q, Witschi MA, Appella DH PNA-DNA duplexes, triplexes, and quadruplexes are stabilized with trans-cyclopentane units. J Am Chem Soc(128): 16456-7, 2006. [Full Text/Abstract]

3. Xu Q, Appella DH Practical synthesis of trans-tert-butyl-2-aminocyclopentylcarbamate and resolution of enantiomers. J Org Chem(71): 8655-7, 2006. [Full Text/Abstract]

4. Hara T, Durell SR, Myers MC, Appella DH Probing the structural requirements of peptoids that inhibit HDM2-p53 interactions. J Am Chem Soc(128): 1995-2004, 2006. [Full Text/Abstract]

5. Myers, M. C.; Wang, J.-L.; Iera, J. A.; Bang. J.-k.; Hara, T.; Saito, S.; Zambetti, G. P.; Appella, D. H.  A New Family of Small Molecules to Probe the Reactivation of Mutant p53 Journal of the American Chemical Society(127): 6152, 2005. [Full Text/Abstract]

6. Pokorski, J. K.; Nam, J.-M.; Vega, R. A.; Mirkin, C. A.; Appella, D. H. Cyclopentane-modified PNA Improves the Sensitivity of Nanoparticle Based Scanometric DNA Detection Chemical Communications: 2101, 2005. [Full Text/Abstract]

7. Lawton, G. R.; Appella, D. H.  Nonionic Sidechains Modulate the Affinity and Specificity of Binding between Functionalized Polyamines and RNA Journal of the American Chemical Society(126): 12762, 2004. [Full Text/Abstract]

Page last updated: December 15, 2008

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