Chimeric platinum-polyamines and DNA binding. Kinetics of DNA interstrand cross-link formation by dinuclear platinum complexes with polyamine linkers.

TLDR: The first observation of a polyamine-DNA interaction using 2D HSQC NMR spectroscopy allows study of the role of the linker in polynuclear platinum-DNA interactions and a novel "anchoring" of the polyamine by Pt-DNA bond formation allows examination of the details of conformational B → Z transitions induced by the polyamines.

Abstract: The first observation of a polyamine–DNA interaction using 2D [1H, 15N] HSQC NMR spectroscopy allows study of the role of the linker in polynuclear platinum-DNA interactions and a novel “anchoring” of the polyamine by Pt–DNA bond formation allows examination of the details of conformational B → Z transitions induced by the polyamine. The kinetics and mechanism of the stepwise formation of 5′-5′ 1,4-GG interstrand cross-links (IXLs) by fully 15N-labeled [{trans-PtCl(15NH3)2}2{μ-(15NH2(CH2)615NH2(CH2)615NH2)}]3+ (1,1/t,t-6,6, 1) and [{trans-PtCl(15NH3)2}2{μ-(15NH2(CH2)615NH2(CH2)215NH2(CH2)615NH2)}]4+ (1,1/t,t–6,2,6, 1′) with the self-complementary oligonucleotide 5′-{d(ATATGTACATAT)2} (duplex I) are compared to the analogous reaction with 1,0,1/t,t,t (BBR3464) under identical conditions (pH 5.4, 298 K). Initial electrostatic interactions with the DNA are delocalized and followed by aquation to form the monoaqua monochloro species. The rate constant for monofunctional adduct formation, kMF, for 1 (0.87 M–1 ...

Figures

Table 3. Rate Constants for the Reactions of 1 and 1´ with Duplex I (at 298 K, pH 5.4)a

Figure 2. The aromatic regions of the 1H NMR spectra (600 MHz) of duplex I after the addition of 1 (a) and 1´ (b) for the times shown. Assignments have been made for the monofunctional species, 3/3´, and the bifunctional adduct, 4/4´. Peaks labeled 'o' have been tentatively assigned to adenine bound adducts based on previous assignments.65

Figure 1. 2D [1H, 15N] HSQC NMR (600MHz) spectra recorded at 298K of 1 (a) and 1´ (b) after their addition to duplex I for the times shown. Peaks have been assigned to the Pt-15NH3 and Pt-15NH2 structures shown in Scheme 1. Peaks labeled 'o' are assigned to other products (possibly adenine bound65 - see also Figure 2) and are similar to those observed in the reactions of I with 1,1/t,t10 and 1,0,1/t,t,t.11 The peak labeled 'i' is assigned to a minor polymeric 15N-labeled impurity with dangling amines in the sample of 1´ (see reference 33).

Figure 3. 1H chemical shift changes (Δδ = δ (duplex I: PPC) - δ (duplex I)) seen after the addition of 1 (a) or 1´ (b) to duplex I. Key: circles (brown) H2 protons; squares (red) aromatic H8/H6 protons; × (blue) H41 protons.

Table 1. 1H/15N Chemical Shifts for the Pt–15NH3 and Pt–15NH2 Groups of 1 and 1´ and the Intermediate Species Observed during their Reactions with Duplex I (at 298K, pH 5.4).a Data for 1,0,1/t,t,t and 1,1/t,t are shown for comparison.

Figure 4. 2D [1H, 15N] HSQC NMR (600MHz) spectra of the central –15NH2– region of 1 after its addition to duplex I for the times shown. Peaks have been assigned to the structures shown in Scheme 1.

Full text

Chimeric Platinum-Polyamines and DNA Binding. Kinetics
of DNA Interstrand Cross-Link Formation by Dinuclear
Platinum Complexes with Polyamine Linkers
Author
Ruhayel, Rasha A, Langner, Janina S, Oke, Matilda-Jane, Berners-Price, Susan J
Published
2012
Journal Title
Journal of the American Chemical Society
Version
Accepted Manuscript (AM)
DOI
https://doi.org/10.1021/ja301397h
Copyright Statement
© 2012 Royal Society of Chemistry. This is the author-manuscript version of this paper.
Reproduced in accordance with the copyright policy of the publisher. Please refer to the journal
website for access to the definitive, published version.
Downloaded from
http://hdl.handle.net/10072/48455
Funder(s)
ARC
Grant identifier(s)
DP1095383
Griffith Research Online
https://research-repository.griffith.edu.au

1
Chimeric Platinum-Polyamines and DNA Binding. Kinetics of DNA
Interstrand Crosslink Formation by Dinuclear Platinum Complexes with
Polyamine Linkers
Rasha A. Ruhayel,
†,§
Janina S. Langner,
†,§
Matilda-Jane Oke,
†
and Susan J. Berners-Price
*,†,§
†
School of Biomedical, Biomolecular & Chemical Sciences, The University of Western Australia, 35 Stirling
Highway, Crawley WA 6009 Australia
§
Institute for Glycomics, Gold Coast Campus, Griffith University, Queensland, 4222, Australia
Ibrahim Zgani
and Nicholas P. Farrell
*
Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia, 23284-2006 USA
§
Present address: Institut für molekulare Biowissenschaften, Goethe Universität, Max-von-Laue Str. 9, 60438
Frankfurt am Main, Germany

2
ABSTRACT: The first observation of a polyamine-DNA interaction using 2D [
1
H,
15
N] HSQC
NMR spectroscopy allows study of the role of the linker in polynuclear platinum-DNA
interactions and a novel “anchoring” of the polyamine by Pt-DNA bond formation allows
examination of the details of conformational B→Z transitions induced by the polyamine. The
kinetics and mechanism of the stepwise formation of 5´–5´ 1,4–GG interstrand cross-links (IXLs)
by fully
15
N-labeled [{trans-PtCl(
15
NH
3
)
2
}
2
{
µ
-(
15
NH
2
(CH
2
)
6
15
NH
2
(CH
2
)
6
15
NH
2
)}]
3+
(1,1/t,t-6,6, 1)
and [{trans-PtCl(
15
NH
3
)
2
}
2
{μ-(
15
NH
2
(CH
2
)
6
15
NH
2
(CH
2
)
2
15
NH
2
(CH
2
)
6
15
NH
2
)}]
4+
(1,1/t,t–6,2,6, 1´)
with the self complementary oligonucleotide 5'-{d(ATATGTACATAT)
2
} (duplex I) are compared
to the analogous reaction with 1,0,1/t,t,t (BBR3464) under identical conditions (pH 5.4, 298 K).
Initial electrostatic interactions with the DNA are delocalized and followed by aquation to form
the monoaqua monochloro species. The rate constant for monofunctional adduct formation, k
MF
,
for 1 (0.87 M
-1
s
-1
) is 3.5 fold higher than for 1,0,1/t,t,t (0.25 M
-1
s
-1
) (the value could not be
calculated for 1´ due to peak overlap). The evidence suggests that several conformers of the
bifunctional adduct form, whereas for 1,0,1/t,t,t only two discrete conformers were observed. The
combined effect of the conformers observed for 1 and 1´ may play a crucial role in the increased
potency of these novel complexes compared to 1,0,1/t,t,t. Treated as a single final product, the rate
of formation of the 5´–5´ 1,4–GG IXL, k
CH
, for 1 (k
CH
= 4.37 × 10
-5
s
-1
) is similar to that of
1,0,1/t,t,t, whereas the value for 1´ is marginally higher (k
CH
= 5.4 × 10
-5
s
-1
).

3
INTRODUCTION
Targeting DNA has contributed significantly to the development of the current anticancer drug
armamentarium and DNA remains a clinically important target.
1,2
DNA-binding drugs interact by
the three “classical” binding modes of intercalation, groove recognition and covalent binding.
Modulation of the inherent lack of tumor specificity of drug action, often using modern advances
in molecular biology, has led to many imaginative approaches such as enhancing sequence
specificity, delivery of site-specific drugs, and metabolic and/or photo-activation.
1-3
Concomitantly, there has been continued discovery of new molecular mechanisms by which small
molecules recognize or interact with DNA.
2
Especially, altered DNA conformations through new
binding modes are also inspirational for new drug design. The targeting of intermediate DNA
structures other than the canonical B-DNA may produce profiles of biological activity hitherto
unknown as well as having broad applications in materials science, biology and medicine.
2,4,5
The acceptance of DNA as cellular target for the anticancer drug cisplatin and its structural
analogs has led to detailed understanding of their modes of DNA binding, the consequent DNA
structural perturbations and protein recognition, as well as effects on cellular signaling pathways.
6,7
Structurally novel drugs, discrete from cisplatin and its analogs in both chemical structure and the
nature of the Pt-DNA adduct, may expand the biological profile of platinum anticancer agents by
circumventing and/or complementing cisplatin-specific biological processes such as DNA repair
or indeed cellular accumulation pathways. Proof of principle of the utility of this approach is
afforded by the advance of BBR3464, the trinuclear, bifunctional DNA binding agent [{trans-
PtCl(NH
3
)
2
}
2
(
µ
-trans-Pt(NH
3
)
2
{NH
2
(CH
2
)
6
NH
2
}
2
)]
4+
(1,0,1/t,t,t or BBR3464) to Phase I and II
clinical trials, the only non-cisplatin analog to be introduced to humans.
8

4
BBR3464 belongs to the general class of polynuclear platinum complexes (PPCs), where two
or three platinum coordination units are linked through flexible diamine chains. These PPCs
comprise a structurally discrete class of platinum-based anticancer agents,
8
and the elucidated
modes of DNA binding are also very distinct.
9
BBR3464 forms long-range {Pt,Pt} interstrand
crosslinks on guanine residues in duplex DNA.
10,11
The formation of “directional” isomers, where
crosslinks are formed in both the 5´ → 5´ and the unusual antiparallel 3´ → 3´ direction, is a
unique feature of the DNA binding of polynuclear compounds.
12,13
A second property of the DNA
adduct structures is that the conformational changes are delocalized, with the syn nucloside
conformations induced even in non-platinated purines.
9,14
The combined effects of the structural
distortions of the 1,4-interstrand crosslink (1,4-IXL) indicate a delocalized, conformationally
flexible “Z-like” lesion, with structural changes transmitted beyond the binding site. This contrasts
with the major 1,2-intrastrand adduct of cisplatin which, although bending the helix significantly,
maintains the B-form in solution.
15,16
Gel retardation assays showed only very weak recognition of
1,4-IXLs by high mobility group HMG1 proteins,
12
which recognize the 1,2-intrastrand adduct and
whose action is implicated in the cytotoxicity of cisplatin.
17,18
Differential protein recognition
represents a molecular mechanism for differentiation of further downstream effects of the
mononuclear and polynuclear adducts. The comparison between mononuclear and polynuclear
platinum presents a good example of the general concepts discussed above.
The charged central linker has been implicated in electrostatic pre-associative interactions in
the minor groove with duplex DNA (specifically to adenine H
2
protons) as well as in the final
bifunctional adducts.
11,14,19,20
Incorporation of a linear polyamine, such as spermidine or spermine,
into the basic polynuclear framework by replacement of the central tetraa(m)mine unit of PPCs
produces a series of dinuclear compounds which replicate the biological activity of the trinuclear