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Combined theoretical and computational study of interstrand DNA guanine–guanine cross-linking bytrans-[Pt(pyridine)2] derived from the photoactivated prodrugtrans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]

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Tai, Hui-Chung, Brodbeck, Ralf, Kasparkova, Jana, Farrer, Nicola J., Brabec, Viktor, Sadler, P. J. and Deeth, Robert J.. (2012) Combined theoretical and computational study of interstrand DNA guanine–guanine cross-linking bytrans-[Pt(pyridine)2] derived from the photoactivated prodrugtrans,trans,trans-[Pt(N3)2(OH)2(pyridine)2]. Inorganic Chemistry, Vol.51 (No.12). pp. 6830-6841. ISSN 0020-1669

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Abstract

Molecular modeling and extensive experimental studies are used to study DNA distortions induced by binding platinum(II)-containing fragments derived from cisplatin and a new class of photoactive platinum anticancer drugs. The major photoproduct of the novel platinum(IV) prodrug trans,trans,trans-[Pt(N3)2(OH)2(py)2] (1) contains the trans-{Pt(py)2}2+ moiety. Using a tailored DNA sequence, experimental studies establish the possibility of interstrand binding of trans-{Pt(py)2}2+ (P) to guanine N7 positions on each DNA strand. Ligand field molecular mechanics (LFMM) parameters for Pt–guanine interactions are then derived and validated against a range of experimental structures from the Cambridge Structural Database, published quantum mechanics (QM)/molecular mechanics (MM) structures of model Pt–DNA systems and additional density-functional theory (DFT) studies. Ligand field molecular dynamics (LFMD) simulation protocols are developed and validated using experimentally characterized bifunctional DNA adducts involving both an intra- and an interstrand cross-link of cisplatin. We then turn to the interaction of P with the DNA duplex dodecamer, d(5′-C1C2T3C4T5C6G7T8C9T10C11C12-3′)·d(5′-G13G14A15G16A17C18G19A20G21A22G23G24-3′) which is known to form a monofunctional adduct with cis-{Pt(NH3)2(py)}. P coordinated to G7 and G19 is simulated giving a predicted bend toward the minor groove. This is widened at one end of the platinated site and deepened at the opposite end, while the P–DNA complex exhibits a global bend of 67° and an unwinding of 20°. Such cross-links offer possibilities for specific protein–DNA interactions and suggest possible mechanisms to explain the high potency of this photoactivated complex.

Item Type: Journal Article
Subjects: Q Science > QD Chemistry
Q Science > QP Physiology
Divisions: Faculty of Science > Chemistry
Library of Congress Subject Headings (LCSH): DNA-protein interactions, Molecular dynamics -- Simulation methods, G proteins, Antineoplastic agents, Cisplatin, DNA adducts
Journal or Publication Title: Inorganic Chemistry
Publisher: American Chemical Society
ISSN: 0020-1669
Official Date: 2012
Volume: Vol.51
Number: No.12
Page Range: pp. 6830-6841
Identification Number: 10.1021/ic3005745
Status: Peer Reviewed
Publication Status: Published
Access rights to Published version: Restricted or Subscription Access
Funder: Overseas Research Students Awards Scheme (ORSAS), University of Warwick Postgraduate Research Scholarship, Engineering and Physical Sciences Research Council (EPSRC), European Research Council (ERC), Grantová agentura České republiky [Grant Agency of the Czech Republic] (GACR), Advantage West Midlands (AWM)
Grant number: EP/F042159 (EPSRC), 247450 (ERC), P301/10/0598 (GACR)
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URI: http://wrap.warwick.ac.uk/id/eprint/48023

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