Individual Final Project

HTGAA 2026 Individual Final Project Documentation

Bio-Hybrid Designer

I. Short Final Project Description

Bio-Hybrid Designer is an AI-powered BioCAD software specifically engineered to design and optimize hybrid biosynthetic pathways for complex natural drugs, such as taxanes (paclitaxel). The tool identifies the optimal transition point where biological synthesis should stop—producing an advanced precursor like baccatin III—and selective chemical synthesis should take over to resolve critical enzymatic bottlenecks, such as poor cytochrome P450 expression in microbial hosts.

II. Final Project Aims

Aim 1: Predictive Validation and Identification of Intermediates

Sub-aim 1.1: Integrate standardized quantitative databases (e.g., BioNumbers, iGEM Registry).
Sub-aim 1.2: Develop ODE models to simulate metabolic flux and identify bottlenecks.
Sub-aim 1.3: Perform in silico simulations to identify optimal intermediates.

Aim 2: Implementation in Secure Microbial Chassis

Sub-aim 2.1: Test codon-optimized genes in E. coli / yeast.
Sub-aim 2.2: Validate predictions experimentally.
Sub-aim 2.3: Integrate kill-switches for biosafety.

Aim 3: Global Democratization and Transition

Sub-aim 3.1: Expand to diverse natural products.
Sub-aim 3.2: Deploy Bioeconomy Transition Fund.
Sub-aim 3.3: Develop decentralized production networks.

III. Outline for Methods (Aim 1)

Step	Technical Action	Tools / Resources
Data Mining	Extract kinetic constants and parameters	BioNumbers, Literature
Flow Modeling	Define pathways & mass balance equations	SBML, MATLAB
Hybrid Simulation	Compare biosynthesis vs hybrid route	AI Algorithms
Security Screening	Analyze sequences for dual-use risks	Biosecurity protocols

IV. Three Incorporated Class Instances

Engineering and Modeling: DBTL cycle and ODE-based predictions.
Foundational Technologies: Codon optimization and DNA synthesis.
Governance and Society: Biosecurity-by-design and global equity.

V. Governance and Society (Ethics Component)

1. Policy and Governance Goals

Enhance Biosecurity: Prevent harmful biological designs via AI filters.
Ensure Global Equity: Protect livelihoods of traditional communities.

2. Proposed Governance Actions

Technical: AI dual-use sequence screening.
Economic: Transition Fund for local communities.
Normative: Mandatory kill-switch standards.

3. Prioritization and Trade-offs

A combined strategy is prioritized. While strict regulatory filters may initially slow research, they are essential for long-term viability and maintaining public trust in synthetic biology.