Using an enzyme to battle the Big C

Cancer is arguably the biggest medical mystery the world is trying to solve today. And researchers like Debopriya Sadhukan from the IITB-Monash Research Academy are attempting to understand the chemistry of cancer, which will hopefully help design better drugs to beat this dreaded disease.

Debopriya’s project is titled ‘Understanding the reaction mechanism of C5-cytosine DNA methyl transferase’.

Possible sites for DNA methylation

“DNA methylation—a process by which methyl groups are added to the DNA molecule—plays a crucial role in carcinogenesis,” she explains, “for it controls gene expression and maintains genome integrity. In tumour cells the normal methylation pattern is disrupted by hypomethylation or region-specific hypermethylation. In such cells, the methylation pattern is controlled by the enzyme C5-cytosine DNA methyltransferase. But how the enzyme catalyses the reaction is still a mystery. We are therefore trying to understand the working mechanism of this enzyme.”

Some of the questions researchers in this field are grappling with are:

i) How is the cysteine residue de-protonated?
ii) What is the role of the Glu119 residue?
iii) What is the nature of the base that will abstract the proton from the 5-position of cytosine?

Says Debopriya, “We are trying to understand the reaction mechanism of this enzyme by a completely different approach so that we can give a much better and easier explanation of the mechanism. In mammals this methylation mostly occurs at the 5-position of cytosine, so our work is solely focused on the reaction mechanism of C5- cytosine DNA methyl transferase. We adopted a simple approach. If the deprotonation energy of the C5-H bond is equal to or less than the protonation energy of the base, then the base will be able to abstract the proton from the 5- position of cytosine. So, we calculated the deprotonation energy of the C5-H bond in the presence of different moieties of the active site and the protonation energy of different bases in both gas phase and in a solution. Though we have not yet been able to close in on a suitable base whose protonation energy is more than the deprotonation energy of the C5-H bond, we found that the difference in deprotonation energy and protonation energy decreases when one increases the dielectric constant of the solvent. This is encouraging!”

Scheme-1: General Reaction Mechanism for DNA Methylation

The IITB-Monash Research Academy is a collaboration between India and Australia that endeavours to strengthen scientific relationships between the two countries. Graduate research scholars like Debopriya study for a dually-badged PhD from both IIT Bombay and Monash University, spending time at both institutions to enrich their research experience.

Says Prof Murali Sastry, CEO of the IITB-Monash Research Academy, “Today’s research challenges require a strongly multi-disciplinary approach. And the way in which this Academy has been set up makes it possible for such multi-disciplinary investigations to be carried out. This gives me immense hope that our research scholars will create significant science, societal and industry impact in the future. According to data from the National Cancer Institute, there are 458.4 new cases of cancer per 100,000 men and women per year. What could be more gratifying than if the work by researchers like Debopriya can help reduce that number?”

Research scholar: Debopriya Sadhukan, IITB-Monash Research Academy

Project title: Understanding the reaction mechanism of C5-cytosine DNA methyl transferase.

Supervisors: Prof. G. Naresh Patwari, Dr. Ekaterina Pas

Contact details:

The above story was written by Mr Krishna Warrier based on inputs from the research student, his supervisors, and IITB-Monash Research Academy. Copyright IITB-Monash Research Academy.