The process of coming up with a topic for iGEM 2020 was multifaceted but the need for helping humanity set the tone for our search. We looked at different fields which ran the gamut from bioremediation of nitrates in the soil to degradation of organic matter. There were ideas to deal with diseases that plague humans like Dengue and Malaria. Researching existing solutions made us realise the difficulty of the drug development process. Our project arose out of the need for more effective techniques to speed up drug development. As the alarming upheaval created by the COVID-19 pandemic shattered lives all around us, we felt the urgency required in this field. The havoc wreaked by a tiny virus, bringing life as we know it to a standstill also drove us to refocus our attention on viral diseases, in particular.
Our team was put together as a blend of science enthusiasts coming from different disciplines, with varied interests. However, the exciting field of synthetic biology enabled us to combine diverse approaches. Since the primary idea was to facilitate drug development, we realised that in vitro systems for testing drugs is of paramount importance. Assembling the host and viral determinants and creating an assay system would be possible only through Synthetic biology. The members of our team engaged in modelling had initially been working on a few minor topics to offer background and strengthen the proposal. The pandemic, however, moulded these into much more integral parts of our project. Let us walk you through the process.
Dengue is a mosquito-borne disease which is caused by the dengue virus. Dengue manifests itself with symptoms such as mild rashes, and the fever dies down after a few days. However, in 0.5 to 1% of the cases, it ends up being life-threatening where it can lead to the deadly Dengue Haemorrhagic Fever (DHF) or Dengue Shock Syndrome (DSS), where the body loses water very rapidly (Sanyaolu et al., 2017). The virus shows a diverse clinical picture-making accurate diagnosis difficult and has been declared by the World Health Organization as a “major global public health challenge in the tropic and subtropic nations”. The statistics reveal an ominous picture.
- The incidence of dengue has increased 30 times over the last 50 years.
- Up to 390 million infections are estimated to occur annually around the world, and it is endemic to 129 countries now, putting over half of the world population at risk.
- It is the tenth highest cause of both mortality and morbidity in developing countries and the leading cause of death in children below 15 years old in some South-East Asian countries (Global Health Data Exchange Results Tool, IHME, 2017).
- In India, certain states which had no reported cases before, including Odisha have now been reporting a widespread incidence of dengue. The surge in cases is attributed to several factors including increased population growth rate, global warming, the spike in urbanization and lack of health care amenities. A lack of awareness on the part of the masses and higher authorities is reflected in poor and inefficient mosquito control programs which aggravate the issue.
To gain a quantitative understanding of the severity of the problem, we looked into the epidemiology of the dengue virus. By mining data from several published papers and national archives, we examined past trends and the increasing incidence of Dengue fever.
After gaining a comprehensive understanding of the past, we tried to understand what the future holds. To see how serious the issue is we tried predicting the burden of the disease using a modified Susceptible-Infected-Recovered (SIR) plot.
Figure 1: The SIR plot represents the infected curve along with the present number of cases. (Refer Epidemiology section to know more).
What did we see? The number of infected people reaches a maximum of around 4,00,000 considering an initial seed population of 96,00,00,000 . Check the epidemiology section for the details regarding how we went about doing it.
Our aim is to initiate a two pronged approach to provide a solution to drug development delays. As proof-of-concept we will carry out our work on the Dengue disease.
Firstly, in the essence of iGEM, we will be using synthetic biology to partially replicate the infection state where the virus interacts with the host system to gain entry and invade the tissues. So, even without using cells isolated from patients, we can create an artificial system that will enable us to study the components of our choice reasonably.
For this, we are creating a modular reporter system consisting of viral components and host components fused to fluorescent tags and assembled in a mammalian expression system. The interaction will be modulated by the use of chemical biology tools. This interdisciplinary approach will provide us with … FRaPPe! A FRET Based Ranker for Proteins and Peptides.
And, to kill two birds with one stone, FRaPPe can eventually turn into a drug screening module to provide a therapeutic intervention strategy for not just Dengue but also several other viral infections. We will use it to test inhibitors designed against specific host-viral interacting components in the Dengue disease. (See schematics for the overall workflow)
Our second approach is to tackle the social aspect of the problem by creating awareness about the disease, the causes and prevention strategies by reaching out to the community at large.
Figure 2: Strategy for FRaPPe reporter system development
Figure 3: Strategy for inhibitory peptide (iPEP) designing and testing using FRaPPe