Team:IISER Bhopal/Safety Safe by design

iGEM 2020 || IISER_Bhopal Safe by Design

Safe By design

THE BIG PIE is focused more on the therapeutics and healthcare track. This made it imperative for us to design a drug that has lab made bacteria but is absolutely safe and effective for the patient. So we created a Safe By Design System to ensure safety for all the concerns we had in mind.

Interaction With Body Environment

1. Pathogenicity

Our interaction with the public showed us that the general opinion about bacteria was that it is bad for us or “pathogenic”. Keeping this in mind, we decided to use Ecoli Nissle, which is Gram-Negative and is a widely known probiotic. With its applications in treating other intestinal ailments and the protection, it provides to the gut. E.coli Nissle would be seen as friendly and safe probiotic instead of a “pathogen”. (Your friendly next-door neighbour!)

2. Delivery

a) Enteric coating Capsule

The objective of our project is to ensure maximum bacterial population interacts with the crypts in the duodenum. This is only possible if the pill dissolution happens in the stomach which would make it susceptible to our bacteria. However after discussion with the drug delivery designer, we were able to come up with the perfect solution which involved pill dissolution at pH= 5.5 and above. This ensures the pill dissolution begins the moment fluids are released from the stomach maintaining safety of the organ, while simultaneously allowing the majority of the bacteria to interact with the duodenum villi.

b) E.coli Nissle

Reprogramming of gut cells into islet cells has previously been done using adenovirus vectors. Creating a drug that is unsafe for oral administration would make it ineffective for the patients. But the usage of E. Coli Nissle as our probiotic delivery vector which is widely found in the human gut microbiome makes the drug delivery safe and reliable.

c) Immune Response

The introduction of foreign vectors into the gut could lead to possible immune responses due to the sensitivity and alertness of the small intestine. Furthermore, an immune response to our system might lead to premature clearance, making our delivery vector less effective. Hence E.coli Nissle would again be the perfect candidate due to its probiotic characteristics which make it safe and have been known to show no known immune response in the gut[1]. To ensure that the adaptive immune system does not compromise either our chassis or our transformed cells, we intend to explore tolerogenic strategies such as tolerogenic DC therapy or thymic display in the future. Risk mitigation via T3SS-mediated tolerance induction, and the use of minicell-based vehicles to minimise immunogenicity, are also potential solutions to the problem.

Interaction within the Gut


We wanted to ensure the safety of the entire human body, by allowing our bacteria to interact with the exact cell type that we aim to reprogramme. We have a 3 step system explained in detail in the Design Section to make the delivery super specific removing the possibility of impacting any other cell type inside the patient.

Safety in the Gut

Keeping in mind safety at all points inside and outside the body. We had to think of a way to make the delivery in the target region safe and reliable. To ensure there is no horizontal gene transfer between microbes with gut microbiomes, we’ve decided to incorporate all the gene sequences into the chromosomes itself, thus removing our dependence on the plasmids.

Microspheres in Enteric capsule

PEG coated microspheres penetrate the mucous of the epithelium and the bacteria are released in the crypt cells in the duodenum. Thus ensuring safety of the gut from our live drug and target niche specificity.

Interaction outside the Body

Environmental safety and Biocontainment

It refers to the release of our GMOs into the environment. There have been several concerns raised regarding the safety of GMO release into the environment. Keeping this in mind, we designed a Kill switch that not only dies as soon as it leaves the human gut but also reduces the activity of our bacteria as soon as it moves out of the small intestine towards the colon.