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This Sandbox is Reserved from January 19, 2016, through August 31, 2016 for use for Proteopedia Team Projects by the class Chemistry 423 Biochemistry for Chemists taught by Lynmarie K Thompson at University of Massachusetts Amherst, USA. This reservation includes Sandbox Reserved 425 through Sandbox Reserved 439.

Structure of Oligonucleotide/Drug complex (1xcs)Structure of Oligonucleotide/Drug complex (1xcs)[1]

by Michael Beauregard, Annie Burton, Jianlong Li, Daniel Marco, and Nathaneal Park

Student Projects for UMass Chemistry 423 Spring 2016 <StructureSection load='1xcs' size='350' side='right' caption='caption for Molecular Playground (PDB entry 1xcs)' scene='48/483883/Homecomplex/2'>

IntroductionIntroduction

The intercalation of DNA and drug compounds has been studied thoroughly; in this case the nucleotide d(CGTACG) was complexed with an anthraquinone derivative. This derivative, 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione, provided researchers with the information needed to solve using X-Ray crystallography. Along with the structure, the important forces involved in binding were analyzed and described as heavily reliant on cations. Furthermore, the binding site seems to be specific to anthracene and similar molecules. Therefore, the potential for drug compounds to be carried by this nucleotide complex requires further research.

Overall StructureOverall Structure

The 1xcs (model at right) complex is a small, simple globular DNA-drug complex, and as such lacks any traditional protein structures such as secondary beta sheets or alpha helices. The complex consists of two complimentary strands of DNA. A simplified model of 1xcs is shown with the nitrogenous bases removed for clarity. The deoxyribose backbones can be followed from 5' to 3' following along each strand from blue to red. Note that the strands are antiparallel where they are (hydrogen) bonded. visualizes this bonding in the middle region of the complex, again following each strand from blue to red from 5' to 3' ends.

The 1xcs complex also binds to metal ions in more than one location, which have been shown to be important to the drug's binding ability. Different metal ions may be present, including Na(+) and Co(2+). These metal ions sites are colored pink in scene. One other metal binding site was noted, which had the ability to bind . This barium binding site is believed to strengthen the ability of the O6 site to bind cobalt. This ability to strongly bind metal ions was also important for x-ray crystallographic purposes, as it enabled researchers to form crystals of the complex by relying on interactions between neighboring molecules' binding sites.

Binding InteractionsBinding Interactions

There are three main locations where ion ligands bind to the oligonucleotide/drug complex. The key ligand is shown in pink. Its function is to close the drug cavity, holding the anthraquinone derivative in place. It can be an Na(+), Mg(2+), or Ba(2+) ion. The two other ligands, shown in cyan bind four to five nucleotides away from the drug itself. Co(2+) ions were always present at these locations in this complex and in similar complexes. Complexes that did not contain Co(2+) did not diffract. Literature states that the variable ion gives strength to the binding of the Co(2+) ions. It may be reasoned that this interaction may also behave oppositely. The binding of the Co(2+) ions may strengthen the closure of the pocket containing the drug. Co(2+) and Ba(2+) ions were found in more locations that are not shown here because they only appeared sporadically and in differing locations. Therefore, they are probably not precisely important to the function of this drug complex.

Additional FeaturesAdditional Features

In , one can see that the anthraquinone derivative is located between the backbones and base pairs of DNA. The drug is squeezed or intercalated between the nucleotides . In the human body, the would also be interacting with the drug shown in black, but in order for this complex to be studied, a short segment of DNA had to be used. Consequently the gold nucleotide is involved in abnormal molecular interactions and is out of place. This intercalation interrupts the function of taq polymerase and telomerase. Taq polymerase is in part responsible for the replication of DNA and consequently, cell replication. Telomeres are repeating sections of non-coding DNA that protect the ends of coding sections of DNA from degradation. Each time a cell divides, telomeres shorten. Over time, telomeres shorten to the point of disappearance, causing DNA degradation and cell death. Telomerase builds up these protective sections of DNA. Cancer is characterized as an uncontrolled rate of cell growth. By inhibiting the replication DNA and the construction of protective telomeres, this drug serves to slow and stop cancerous cell growth.

Quiz Question 1Quiz Question 1

A unique site is the __ ion found associated with the , which gives additional strength to the guanine–Co2+–guanine interaction. A Mg2+ B Co2+ C Ba2+ D Mg2+

See AlsoSee Also

• 1bp8
• 1d3x
• 1p3x

CreditsCredits

Introduction - Daniel Marco

Overall Structure - Nathaneal Park

Drug Binding Site - Annie Burton

Additional Features - Michael Beauregard

Quiz Question 1 - Jianlong Li

ReferencesReferences

Human Telomerase Inhibition by Regioisomeric Disubstituted Amidoanthracene-9,10-diones Philip J. Perry,†, Anthony P. Reszka,†, Alexis A. Wood,†, Martin A. Read,†, Sharon M. Gowan,‡, Harvinder S. Dosanjh,†, John O. Trent,†,§, Terence C. Jenkins,†,‖, Lloyd R. Kelland,‡ and, and Stephen Neidle*,† Journal of Medicinal Chemistry 1998 41 (24), 4873-4884 DOI: 10.1021/jm981067o