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

Abstract

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 Ka ) 5.2 × 10 8 M -1 for 28-mer hairpin) by m-OH increases the AATT site binding energy by 1.1 kcal mol -1 , Ka ) 3.8 × 10 9 M -1 . Addition of a second m-hydroxy group (bis-m-OH Hoechst) further strengthens binding, giving Ka ) 1.9 × 10 10 M -1 , and the binding energy increases by about 2.1 kcal mol -1 compared to p-OH Hoechst. The value of Ka 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.

The Fluorophore 4′,6‐Diamidino‐2‐phenylindole (DAPI) Induces DNA Folding in Long Double‐Stranded DNA

“…The kinetic study of the system shows that two different kinetic effects are present: the fast one is concluded in the millisecond time range, the slow one is much slower (1 s). Both intercalation and groove binding are fast reactions, the latter being often nearly diffusion controlled 37. Therefore, the fast effect will reflect the sum of both DAPI groove binding and intercalation.…”

Mechanistic aspects of the interaction of intercalating metal complexes with nucleic acids

“…The time constant of this additional effect, being far below any time constant measured for intercalation of simple drugs into nucleic acids, suggests a wide alteration of the polymer cavity in order to introduce the metal containing residues. The alternative explanation based on groove binding can be discarded on the basis of the kinetic results, as these binding modes have been shown to be nearly diffusion controlled [127]. Therefore, the proposed reaction mechanism for both DNA/Pt-PR and poly(A)·poly(A)/Pt-PR systems is a three-step sequential pathway (Scheme (12)) D + S DS I DS II DS III (12) where DS I represents a partial intercalate, that converts into a complex (DS II ) where the proflavine residue fully penetrates between the base pairs.…”

Binding of netropsin to several DNA constructs: Evidence for at least two different 1:1 complexes formed from an –AATT-containing ds-DNA construct and a single minor groove binding ligand

“…It is generally believed that water plays an important role in a number of biological reactions including the binding of small molecules to proteins [1][2][3][4][5], the interactions of small molecules with nucleic acids [6][7][8][9][10][11][12][13][14], the folding or unfolding of proteins [15,16] and the interaction of proteins with DNA [17][18][19][20][21][22]. In most cases the water under discussion is water of solvation or hydration of the macromolecule and to a smaller degree the ligand.…”