Experimental Precedent for the Need To Involve the Primary Hydration Layer of DNA in Lead Drug Design

The increase in fluorescence on binding of m-phenyl substituted hydroxy derivatives of Hoechst 33258 with poly[d(A−T)], d(CGCGAATTCGCG)2, and with the corresponding T4-looped 28-mer AATT hairpin was used to monitor binding by equilibrium titrations and stopped-flow kinetics. Replacing the p-OH subst...

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Bibliographic Details
Published in:Journal of medicinal chemistry 2001-08, Vol.44 (16), p.2503-2506
Main Authors: Breusegem, Sophia Y, Sadat-Ebrahimi, Seyed E, Douglas, Kenneth T, Bichenkova, Elena V, Clegg, Robert M, Loontiens, Frank G
Format: Article
Language:English
Subjects:
Antineoplastic agents
Biological and medical sciences
Bisbenzimidazole - chemistry
DNA - chemistry
Drug Design
Fluorescent Dyes - chemistry
Fundamental and applied biological sciences. Psychology
General aspects
Interactions. Associations
Intermolecular phenomena
Kinetics
Medical sciences
Molecular biophysics
Oligonucleotides - chemistry
Pharmacology. Drug treatments
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Summary:The increase in fluorescence on binding of m-phenyl substituted hydroxy derivatives of Hoechst 33258 with poly[d(A−T)], d(CGCGAATTCGCG)2, and with the corresponding T4-looped 28-mer AATT hairpin was used to monitor binding by equilibrium titrations and stopped-flow kinetics. Replacing the p-OH substituent of Hoechst 33258 (association constant K a = 5.2 × 108 M-1 for 28-mer hairpin) by m-OH increases the AATT site binding energy by 1.1 kcal mol-1, K a = 3.8 × 109 M-1. Addition of a second m-hydroxy group (bis-m-OH Hoechst) further strengthens binding, giving K a = 1.9 × 1010 M-1, and the binding energy increases by about 2.1 kcal mol-1 compared to p-OH Hoechst. The value of K a determined at equilibrium equaled that determined from the ratio of association and dissociation rate constants from stopped-flow studies. The increase in affinity of the monohydroxy Hoechst analogue (m-OH) may originate from water-mediated hydrogen bonding with the minor groove. The further increase in affinity of the bis-m-OH derivative (whose second m-OH group must be directed away from the DNA minor groove floor) may arise from a hydrogen-bonded network of water molecules. The potential to increase binding strength through relayed water molecules is proposed as an additional possible input for lead drug design at DNA targets.
ISSN:0022-2623
1520-4804
DOI:10.1021/jm0100943