Four-stranded DNA structures known as G-quadruplexes, which  are present in human genome, can control the activities of cancer-causing genes and hence have emerged as anticancer drug targets.

Scientists at the Indian Association for the Cultivation of Science, Jadavpur, Kolkata have used a novel approach to drug discovery by attaching or linking a DNA sequence of interest to gold-coated magnetic nanoparticles and picking those molecules that target and bind to the DNA sequence for further study. This approach helps in rapid identification of potential DNA binding molecules for cancer therapy. The results were published in the journal Nature Communications.

G-quadruplexes are four-stranded DNA structures found in human genome, for example, the presence of G-quadruplexes in cancer-causing gene c-MYC. Since G-quadruplexes are involved in regulation of the gene expression, there is increased interest in finding molecules that target them.

The traditional approach is to synthesise compounds and study their interactions with drug targets before choosing the best drug molecules. This is both time consuming and laborious.

So a team led by Prof. Jyotirmayee Dash from the Department of Organic Chemistry at IACS first immobilised the G-quadruplex DNA onto gold-coated magnetic nanoparticles and left the target in a solution containing azide and alkyne functional groups.

Quicker selection of molecules

The azide and alkyne fragments that are capable of binding to the adjacent sites of the G-quadruplex react with each other to produce triazole products. Theoretically, the combination of azide and alkyne fragments can generate 66 triazole products. “Since the G-quadruplex itself selects the azide and alkyne building blocks, only three triazole compounds were formed that can interact with the G-quadruplex target. The unreacted fragments could be easily removed,” says Prof. Dash who is the corresponding author of the paper. Prof. Dash is a recipient of DST’s Swarnajayanti Fellowship and carried out this work using this funding.

Interestingly, the DNA nano-template can be recovered and reused multiple times. When the nanoparticles are heated, the triazole products that are bound to the G-quadruplex target get detached and get into solution. Since the DNA-linked, gold-coated magnetic nanoparticles  (DNA nano-template) are used, they can be separated from the solution using magnetic separation. “The DNA nano-templates can be reused up to five times,” she says.

The researchers found that of the three triazole compounds that selectively bound to the G-quadruplex target, one (Tz 1) was found in large proportion and was the only molecule that was obtained when the nanoparticle was recycled for the fourth and fifth time.

Anti-cancer properties

“We found the Tz 1 molecule has remarkable anti-cancer properties. The molecule binds to the G-quadruplex and is able to switch off the c-MYC gene that gets over-expressed in breast, colon and lung cancer. We studied the effect of Tz 1 molecule using colon cancer cell lines and found the molecule was able to inhibit cancer growth and ultimately kill colon cancer cells,” Prof. Dash says. “The molecule preferentially binds to the G-quadruplex DNA and not the duplex DNA. Further, the molecule selectively kills the cancer cells, without doing any harm to the normal cells.” The Tx 1 molecule was found to permeate cell and nuclear membranes and preferentially localize in the nuclei of the cells and induce apoptosis.

“Based on the extremely high cellular activity of identified drug compound, we can conclude that this methodolgy using DNA nano-template allows easy synthesis of high-affinity drug molecules for the target DNA without performing any conventional drug synthesis procedures,” she says. “Though this study is a proof-of-concept, this approach can be used for economical and fast screening of potential drug candidates for other DNA targets, RNA and even proteins.”

Published in The Hindu on July 22, 2017