Antigene Strategy in Breast Cancer Therapy: Rationales for Direct Targeting of erbB2/Her2 DNA with Polyamides.

摘要

The major goal of this project is to design and computationally evaluate the most potent Pyrrole-Imidazole containing polyamide inhibitors of erbB2/Her2 transcription. In the first year of the project we used an original algorithm to identify the most suitable sequences within erbB2 promoter DNA to target with the polyamides. This year we focused our efforts on generating polyamides with high affinity and specificity to the target DNA sequences. Thus, we have developed an improved and extended version of our algorithm to build 3- Dimentional molecular models of polyamides bound into the minor groove of DNA. In this algorithm, a standard B-DNA model is used as initial conformation for double stranded DNA, and the polyamide chain is placed in the minor groove according to the specified polyamide-DNA pairing rules. Geometries of these initial conformations are energy optimized under special distance constraints, derived from the available polyamide-DNA x- ray structures. The improved approach provides reliable models for longer complexes and allows to include new elements into polyamide design. In addition we developed a fast method to introduce 'mismatches' into the DNA sequence of the model and evaluate their effect on affinity of the complex. Systematic study of DNA-polyamide complex with such mutations can be used to predict binding specificity.