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Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
Published on: January 20, 2016
Effects of N-terminus modified Hx-amides on DNA binding affinity, sequence specificity, cellular uptake, and gene
Konstantinos Kiakos1, Vijay Satam2, Pravin C Patil2
1Cancer Research UK Drug-DNA Interactions Research Group, UCL Cancer Institute, London WC1E 6BT, United Kingdom; Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Waehringer Str. 42, 1090 Vienna, Austria.
New polyamide analogues (X-HxIP) were synthesized to improve DNA binding and topoisomerase IIα (TOP2A) gene modulation. While some analogues showed enhanced DNA binding and specificity, cellular uptake proved critical for biological activity.
Area of Science:
- Medicinal Chemistry
- Molecular Biology
- Genetics
Background:
- Small molecules targeting specific DNA sequences offer therapeutic potential.
- Polyamides are a class of DNA-binding molecules with potential applications in gene regulation.
- Topoisomerase IIα (TOP2A) is a key enzyme in DNA replication and a target for cancer therapy.
Purpose of the Study:
- To design and synthesize novel N-terminus modified X-HxIP analogues.
- To optimize DNA binding affinity and sequence specificity.
- To enhance cellular uptake, nuclear penetration, and TOP2A gene expression modulation.
Main Methods:
- Synthesis of five X-HxIP analogues (6a-e) with varied N-terminus modifications.
- In vitro DNA binding assays to determine affinity and sequence specificity for the TOP2A promoter region.
- Cellular uptake and nuclear penetration studies in human lung cancer cells.
- Assessment of TOP2A gene expression modulation.
Main Results:
- All X-HxIP analogues preferentially bound to the 5'-TACGAT-3' sequence within the TOP2A promoter.
- Analogue 6a showed higher binding affinity and abolished protein:DNA interaction in vitro.
- Analogues 6b-e exhibited improved DNA sequence selectivity but reduced binding affinity.
- Analogue 6a failed to enter cells and modulate TOP2A expression, highlighting the importance of cellular uptake.
Conclusions:
- DNA binding affinity and sequence selectivity are crucial but insufficient for biological activity.
- Cellular uptake and nuclear concentration are critical determinants for achieving desired gene modulation.
- Structural modifications in polyamides significantly impact their biological efficacy, necessitating a holistic design approach.
