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Updated: Jan 11, 2026

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
Published on: January 20, 2016
High-affinity A/T-rich DNA binding with a dimeric bisbenzamidine.
David Bouzada1, Ananya Paul2, Mateo I Sánchez1
1Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain.
Researchers developed a new DNA minor groove binder by dimerizing a bisbenzamidine agent. This enhanced DNA-binding compound shows increased affinity for A/T-rich sites and higher antileishmanial activity.
Area of Science:
- Medicinal Chemistry
- Molecular Biology
- Structural Biology
Background:
- Bisbenzamidine compounds are DNA-binding agents.
- Targeting DNA minor groove offers therapeutic potential.
- Enhancing DNA affinity can improve drug efficacy.
Purpose of the Study:
- To develop a dimerized bisbenzamidine DNA minor groove binder.
- To investigate the compound's DNA binding affinity and specificity.
- To evaluate the antileishmanial activity of the novel agent.
Main Methods:
- Chemical synthesis and dimerization of bisbenzamidine.
- DNA binding assays to determine affinity and specificity.
- Nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulations.
- Antimicrobial assays against Leishmania parasites.
Main Results:
- Dimerized bisbenzamidine showed over 20-fold enhanced DNA affinity.
- High affinity was observed for extended A/T-rich DNA sequences.
- Structural studies revealed minor groove insertion.
- Increased DNA affinity correlated with enhanced antileishmanial activity.
Conclusions:
- Dimerization effectively creates an extended DNA minor groove binder.
- The novel compound exhibits potent antileishmanial activity.
- Structural insights guide the design of future DNA-targeting agents.
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