This project is directed towards the development of protein-detecting micro arrays (PDMs) that will allow the sensitive and quantitative analysis of hundreds or, eventually, thousands of proteins simultaneously. A major obstacle to development of PDMs is the formidable task of isolating and producing in quantity so many different protein-binding agents. It is argued here that while the first generation of such devices will employ antibodies or other macromolecules with antibody-like binding properties, in the long run synthetic protein ligands would be preferred greatly. These could be made more easily and in far larger quantities than biomacromolecules, a critical issue if this technology is to be adopted broadly. A straightforward method to isolate """"""""pincer ligands"""""""" is proposed. These are readily synthesizable molecules consisting of a lead peptide, isolated by phage display, coupled to another peptide or peptide-like compound. These species are anticipated to bind tightly to their target proteins via two point contacts or clamp-like interactions. A novel approach to the high-throughput isolation of such compounds is proposed that obviates many of the problems inherent in current methods used to obtain such ligands. A second issue of critical importance will be to develop methods suitable for monitoring, in a sensitive and quantitative fashion, binding of the proteins in a biological sample to the various capture ligands on the array. We propose a novel magnetic resonance imaging (MRI)-based method to accomplish this task without the need to chemically label the proteins in the sample. Demonstrating the feasibility of these approaches to solving the two most serious roadblocks to the development of PDMs will constitute the R21 phase of this project. If successful, we will then move to apply these technologies to the creation and evaluation of functional PDMs.
| Kodadek, Thomas; Reddy, M Muralidhar; Olivos, Hernando J et al. (2004) Synthetic molecules as antibody replacements. Acc Chem Res 37:711-8 |
| Reddy, M Muralidhar; Bachhawat-Sikder, Kiran; Kodadek, Thomas (2004) Transformation of low-affinity lead compounds into high-affinity protein capture agents. Chem Biol 11:1127-37 |
| Bachhawat-Sikder, Kiran; Kodadek, Thomas (2003) Mixed-element capture agents: a simple strategy for the construction of synthetic, high-affinity protein capture ligands. J Am Chem Soc 125:9550-1 |
| Alluri, Prasanna G; Reddy, M Muralidhar; Bachhawat-Sikder, Kiran et al. (2003) Isolation of protein ligands from large peptoid libraries. J Am Chem Soc 125:13995-4004 |
| Naffin, Jacqueline L; Han, Ying; Olivos, Hernando J et al. (2003) Immobilized peptides as high-affinity capture agents for self-associating proteins. Chem Biol 10:251-9 |
| Kodadek, Thomas (2002) Development of protein-detecting microarrays and related devices. Trends Biochem Sci 27:295-300 |
| De Leon-Rodriguez, Luis M; Ortiz, Alfonso; Weiner, Allison L et al. (2002) Magnetic resonance imaging detects a specific peptide-protein binding event. J Am Chem Soc 124:3514-5 |
| Olivos, Hernando J; Alluri, Prasanna G; Reddy, M Muralidhar et al. (2002) Microwave-assisted solid-phase synthesis of peptoids. Org Lett 4:4057-9 |
