iGEM 2024 — Team afcm-egypt

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# Notebook

![](https://static.igem.wiki/teams/5036/new-headers/notebook.png)

Notebook

Unable to display PDF file. [Download](https://static.igem.wiki/teams/5036/new-protocols.pdf) instead.

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# Engineering

![](https://static.igem.wiki/teams/5036/new-headers/e-s.png)

![](https)[Concept Design](#ConceptDesign)

![](https)[Platform Design](#PlatformDesign)

![](https)[References](#ref)

Engineering Success

## Introduction

This year, our team has focused on the development of an
**individualized cell-based therapy** that can revolutionize the
field of regenerative medicine. We wanted to create an
innovative approach for the enhancement of the healing process
while preventing the various long-term complications following
tissue injury. We focused on the restoration of normal tissue
functions, especially in non-regenerative organs like neural,
cardiac, and dermal tissue of the skin. After deep brainstorming,
we chose burn wounds as a proof of concept for our dynamic
platform, aiming **to optimize burn wound care** and **minimize
disfiguring scarring and contractures**. Our vision is to change
the life of all burn survivors through our stem cell-based,
occlusive, nutritive gel of healing kit, consequently known as
**“SONG-H”**.

Throughout this long journey, we encountered **many challenges**
that regularly redefined the development of our platform. We
relied on deep literature research, many experts integration, in
silico software validation, and finally laboratory experimental
validation. All these obstacles are discussed **along our DBTL cycles**
which lead to essential modifications in our design.

This is a simple tutorial to handle the different stages of our DBTL cycles.

![](https://static.igem.wiki/teams/5036/tutorial.png)

## Concept Design

We started our engineering success with the preliminary
challenges that we faced during the development of our concept.
This development started early after our topic selection phase
where we settled on the induction of healing in non-regenerative
organs as our project for this year. We went through eight
different iterations in order to come out with the safest, most
effective, and dynamic concept design. This concept would
undergo further modifications to produce our innovative stem
cell-based occlusive nutritive gel of healing (SONG-H).

### Iteration 1: Induction of healing in non-regenerative organs

Design
Build
Test
Learn

Despite great global efforts seeking the improvement of healthcare systems, recent studies show the massive impact of irreversible organ damage on the increasing death rates worldwide.

A definitive technology is required to control the heavy burden of non-regenerative tissue injury. In our first iteration, we wanted to develop a new concept enhancing the healing ability of specific organs such as neural, myocardial, and renal tissues.

We started searching the literature for the latest technologies implemented in healing induction processes. These new techniques include stem cell therapy, biological agents, 3D printing, surgical procedures, and gene therapy.

To come up with the most optimized platform for tissue healing, we needed to dig deeper into the benefits and drawbacks of each one of the previously mentioned techniques.

### Iteration 2: Induction of healing through effector genes and proteins

Design
Build
Test
Learn

We wanted to induce self-renewal functions in non-regenerative tissues through a dynamic platform. This technology would be based on the potential of synthetic biology to yield new regenerative functions in irreversibly damaged organs.

We needed to find a delivery system capable of safe transportation of our effector proteins to its target tissues. We concluded that genetically engineered bacteria would be an interesting option to express and deliver our therapeutic agents.

Unfortunately, our literature research proved that bacterial delivery had multiple limitations such as the difficulty to carry large sequences of effector proteins necessary for the healing mechanism. In addition, bacterial products had many unwanted side effects including off-targeting effects, allergic reactions, and immune system suppression.

We discovered that bacterial products are not reliable as a delivery system for our platform due to their undesired limitations and unpreventable drawbacks. Hence, we needed to find another method to ensure safe and effective transportation of our effector proteins.

![](https://static.igem.wiki/teams/5036/limitations-2.png)

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# Experiments

![](https://static.igem.wiki/teams/5036/new-headers/wet-lab.png)

Experiments

Unable to display PDF file. [Download](https://static.igem.wiki/teams/5036/lab/protocols.pdf) instead.

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# Results

![](https://static.igem.wiki/teams/5036/new-headers/results.png)

![](https)[Dry Lab](#drylab)

![](https)[Wet Lab](#wetlab)

Results

## Dry Lab

To ensure the validity of our approach, we engaged dry lab validation in all along our project steps. Initially, we settled a plan for validating the biological systems in our approach. Our plan is to visualize the protein structure, measure the affinity of sensing parts to their ligands, and simulate the human physiological environment to predict its effect on our different biological parts.Hence, we started our dry lab validation of our receptor by homology modelling to visualize our receptor parts:

### External domain:

#### External Domain Molecular docking

After providing the 3D structure, we need to ensure these parts function, which is binding to the VEGFA extracellulary, by performing molecular docking simulation using alpha fold 3 server between VEGFR1 and VEGFA, and between the VEGFR1 and VEGFA to compare between their binding affinities.

- **VEGFR1-VEGFA complex**
![](https://static.igem.wiki/teams/5036/drylab/vegfr1-vegfa-docking-results.png)

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