This research plan represents a first step toward the design of artificial DNA-interactive agents based on protein motifs that closely resemble known antitumor drugs. These studies seek, in the long term, to develop molecules with pharmacological properties based on the hypothesis that agents designed to imitate DNA binding proteins may exhibit a targeted bioactivity with diminished cytotoxicity in comparison to conventional natural products that associate with DNA. The following proposal will investigate synthetic analogues of a tandem beta-turn motif found in RNA polymerase II (Tyr-Ser-Pro-Thr-Ser-Pro-Ser-Tyr) that: 1) closely resembles antitumor agents of the quinoxaline class (i.e., triostins and echinomycin); 2) binds to DNA in a fashion similar to bis-intercalating drugs; and 3) exhibits a selectivity for AT-rich DNA regions. Specifically, the proposed studies will attempt to increase the structural integrity and DNA binding affinity of this naturally-occurring motif through strategic substitutions of natural and unnatural amino acids and peptidomimetics that are known to support a type II beta-turn conformation. The modifications to be employed have been chosen to minimally perturb the peptide nature of these structures while also representing a first step toward the development of agents with drug-like stability and protease resistance. The structures of these redesigned motifs will be investigated using 2D NMR, circular dichroism (CD) spectroscopy, and molecular modeling. In parallel, investigations of DNA sequence-selectivity through hydroxyl radical footprinting techniques and evaluations of their mechanism(s) of nucleic acid binding will be carried out to fully develop a model of beta-turn-DNA interaction(s). These studies are particularly interested in correlating motif structure and conformational rigidity to DNA selectivity and helical distortion. This direction represents a novel approach to the rational design of agents that bind to DNA; while most studies in this area have been aimed at redesigning and understanding natural products that interact with DNA, these studies will harness and improve upon the designs utilized by DNA binding proteins.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
First Independent Research Support & Transition (FIRST) Awards (R29)
Project #
5R29GM050557-02
Application #
2188473
Study Section
Bio-Organic and Natural Products Chemistry Study Section (BNP)
Project Start
1994-08-01
Project End
1999-07-31
Budget Start
1995-08-01
Budget End
1996-07-31
Support Year
2
Fiscal Year
1995
Total Cost
Indirect Cost
Name
Indiana University-Purdue University at Indianapolis
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
005436803
City
Indianapolis
State
IN
Country
United States
Zip Code
46202
Nagane, R; Koshigoe, T; Chikira, M et al. (2001) The DNA-bound orientation of Cu(II)-Xaa-Gly-His metallopeptides. J Inorg Biochem 83:17-23
Huang, X; Pieczko, M E; Long, E C (1999) Combinatorial optimization of the DNA cleaving Ni(II) x Xaa-Xaa-His metallotripeptide domain. Biochemistry 38:2160-6
Brittain, I J; Huang, X; Long, E C (1998) Selective recognition and cleavage of RNA loop structures by Ni(II).Xaa-Gly-His metallopeptides. Biochemistry 37:12113-20
Dobbins, J R; Murali, N; Long, E C (1996) Structural redesign and stabilization of the overlapping tandem beta-turns of RNA polymerase II. Int J Pept Protein Res 47:260-8