Week 1 HW: Final Project Ideas

An Affordable Recombinant Therapeutic Peptide to Support Addiction Recovery

1. What I Would Like to Biomanufacture and Why

I would like to explore the biomanufacturing of a low-cost recombinant therapeutic peptide, formulated as an oral capsule or soluble powder, intended to support people recovering from substance use disorders, particularly alcohol and opioid use disorders.

The Product I Envision

My initial concept is a neuropeptide that modulates the gut-brain axis, based on an optimized variant of known sequences associated with craving regulation and emotional regulation.

The intended product would be stabilized and formulated for daily oral administration.

This is currently a conceptual proposal. I have not yet selected a specific peptide sequence or established that the proposed biological mechanism, oral delivery route, or therapeutic effect will work. These are among the questions I hope to investigate.

Who Would It Serve?

My intended beneficiaries are people undergoing addiction treatment in resource-limited settings, particularly public health programs in Bolivia and Latin America.

As an initial reference population, I envision a pilot serving approximately 1,000 patients.

Why This Problem Matters to Me

Addiction can directly reduce a person’s freedom of action and ability to think clearly. It can progressively limit their capacity to make decisions, maintain relationships, pursue goals, and shape their own future.

For me, this makes substance use disorders not only a medical challenge, but also a challenge to human agency.

Existing biological treatments and supportive interventions can be expensive or difficult to access in many parts of Latin America. I am interested in exploring whether biomanufacturing could help create an affordable biological tool that expands the options available to people in recovery.

My motivation is both practical and personal: as someone with a background in medical devices and artificial intelligence, I want to explore how biological engineering can produce accessible tools that improve people’s ability to participate in their own recovery.

I am not trying to create a single intervention that “cures” addiction overnight. Instead, I want to investigate whether a therapeutic peptide could support craving regulation and treatment adherence alongside existing recovery programs.

My focus is deliberately narrow: developing an accessible biological tool for a specific health problem, rather than attempting to solve every social or institutional factor surrounding addiction.

2. What Living System Would I Use?

I would begin with a microbial production system, complemented by cell-free expression for rapid prototyping.

Main Chassis: Microbial Production

My primary candidates would be:

• Escherichia coli
• Bacillus subtilis, particularly strains suitable for food-related or probiotic applications where appropriate.

The choice would ultimately depend on the peptide’s characteristics, expression requirements, secretion behavior, and downstream purification needs.

Complementary Chassis: Cell-Free Systems

For early prototyping, I would use cell-free expression systems derived from E. coli extracts.

This would allow me to explore candidate sequences and expression strategies without first committing to the construction and optimization of living production strains.

High-Level Biological Workflow

Input

• A synthetic, codon-optimized gene encoding the selected peptide.
• A simple culture medium for microbial production.

For cell-free production, the inputs would include an extract, amino acids, and an appropriate energy regeneration system.

Biological Process

In the microbial system, the gene would be transcribed and translated, with the peptide either secreted or accumulated in an intracellular form such as inclusion bodies.

In the cell-free system, peptide synthesis would occur outside living cells, potentially allowing rapid prototyping within hours.

Output

The intended output would be a crude peptide-containing product that could undergo:

1. Purification through an appropriate downstream process.
2. Stabilization, potentially including lyophilization.
3. Formulation into an oral dosage form.

The exact purification strategy would depend on the peptide’s properties. I would initially explore whether precipitation, relatively simple chromatography, or filtration-based approaches could provide a viable starting point.

Initial Assumptions

Several assumptions guide this concept:

• The peptide could be designed from known sequences associated with gut-brain signaling and craving regulation.
• Computational design or directed evolution might improve its stability and oral bioavailability.
• Appropriate microbial chassis could eventually support a more accessible manufacturing and regulatory pathway.

These remain hypotheses, not established results.

I am intentionally not designing the complete genetic circuit or selecting the final sequence yet. My first objective is to identify a promising biological candidate and determine whether its production and delivery are technically feasible.

3. How Would I Use Automation?

My main automation strategy would combine Cloud Labs, benchtop liquid-handling robots, and automated laboratory fermenters.

I see automation as an essential tool for accelerating the design-build-test cycle, particularly during the development phase.

1. Screening Peptide Variants

I would automate the screening of:

• Peptide sequences and structural variants.
• Promoters and expression strategies.
• Secretion signals.
• Induction conditions.

Cloud Lab infrastructure and liquid-handling robots could allow hundreds of combinations to be evaluated in parallel, reducing the time and manual effort required for experimentation.

2. Optimizing Culture and Fermentation Conditions

I would use automated liquid handling and online sensors to investigate variables such as:

• Temperature.
• pH.
• Culture media.
• Induction timing.
• Other relevant fermentation parameters.

The goal would be to identify conditions that improve peptide production while maintaining consistency and reducing resource consumption.

3. Automating Sampling and Performance Measurements

I would also automate parts of the sampling and analytical workflow, including:

• Scheduled sample collection.
• Peptide quantification.
• Activity assays, where suitable.
• Data collection for comparison between experimental conditions.

This would create a feedback loop between biological experiments and computational analysis.

How My Software Background Fits In

My experience in software development and artificial intelligence makes this particularly interesting.

I would like to explore how computational systems could coordinate experimental design, laboratory automation, data analysis, and decision-making.

For me, automation is not simply about replacing manual work. It is about making biological experimentation more accessible, reproducible, and efficient, while allowing researchers to explore a larger design space than would be practical manually.

During the prototyping stage, Cloud Labs and benchtop liquid-handling robots would be particularly valuable.

At manufacturing scale, however, the focus would shift toward automated fermentation, process monitoring, and bioreactor control. Small liquid-handling robots would play a less central role in producing the final material.

4. How Much Would I Need to Make, and How Long Would It Take?

A. How Much?

I define a meaningful initial scale as treating 1,000 people over a 30-day cycle.

This represents a regional pilot that could be relevant to a public health program in Bolivia.

Dose Assumption

For this preliminary engineering estimate, I assume:

• Daily dose: 0.5 mg of purified peptide per person.
• Treatment population: 1,000 people.
• Treatment duration: 30 days.

The assumed dose is an exploratory estimate informed by reported ranges for certain small peptides discussed in the recovery and therapeutic peptide literature. It is not a clinically validated dose for the proposed product.

Calculation

[ 1,000 \text{ people} \times 0.5 \text{ mg/day} \times 30 \text{ days} ]

[ = 15,000 \text{ mg} = \boxed{15 \text{ g}} ]

Therefore, my initial manufacturing target would be 15 grams of purified peptide for one 30-day cycle.

This calculation excludes formulation losses and additional material for quality control or contingency. A more detailed estimate would likely include an additional 20–30% production margin.

B. How Long Would It Take?

For this preliminary estimate, I assume microbial fermentation using E. coli.

Production Assumptions

The assumed yield is an intermediate engineering estimate. Reported recombinant peptide production yields can vary substantially depending on the peptide, host, expression strategy, and purification process.

Calculation

1. Output per batch

[ 50 \text{ mg/L} \times 10 \text{ L} = 500 \text{ mg} = 0.5 \text{ g} ]

2. Number of batches required

[ 15 \text{ g} \div 0.5 \text{ g/batch} = 30 \text{ batches} ]

3. Number of production cycles with four reactors

[ 30 \div 4 = 7.5 ]

Rounding up, this requires 8 production cycles.

4. Total production time

[ 8 \text{ cycles} \times 3 \text{ days} = \boxed{24 \text{ days}} ]

Under these assumptions, producing the 15 grams required for one 30-day pilot would take approximately 24 days of continuous production.

This is a back-of-the-envelope engineering estimate, not a validated manufacturing schedule. It does not fully account for equipment downtime, quality-control testing, batch failures, or additional formulation and packaging time.

Prototyping Versus Manufacturing

I would deliberately separate the two stages.

Development and prototyping

I would use cell-free expression combined with Cloud Lab infrastructure and liquid-handling robots.

Cell-free systems could be useful for screening because they enable rapid testing of many candidate designs, even if their output is not sufficient for manufacturing tens of grams of product.

Manufacturing

Once a promising peptide and production strategy had been identified, I would transition to microbial fermentation.

At this stage, automated bioreactor control, process monitoring, and downstream purification would become more important than benchtop liquid-handling robots.

What If Production Yield Improves?

If optimization increased the purified yield to approximately 100–200 mg/L, the required fermentation volume and production time could decrease substantially.

This highlights one of the main reasons to invest in automated screening and process optimization early in the project.

5. What Don’t I Know Yet?

The three largest technical unknowns I currently see are the following.

1. Actual Yield and Stability of the Specific Peptide

I do not yet know the actual expression yield or stability of the selected peptide after production, purification, and lyophilization.

I would need to experimentally measure:

• Expression levels.
• Solubility.
• Purity.
• Stability during storage.
• Shelf life under room-temperature conditions.

The assumed 50 mg/L yield is only a starting point for engineering calculations.

2. Oral Bioavailability and Real Biological Activity

I am assuming that a suitably stabilized peptide might retain sufficient activity when administered orally.

However, this is one of the most important uncertainties in the entire concept.

I would need to investigate:

• Stability against intestinal proteases.
• Intestinal permeability.
• Whether the peptide can reach its intended biological target.
• Whether the formulated product produces meaningful biological activity.
• Whether any observed activity translates into effects relevant to craving or gut-brain signaling.

This would require progressive validation, beginning with appropriate in vitro studies and potentially advancing to in vivo research under the necessary ethical and regulatory frameworks.

3. Low-Cost Purification and Regulatory Feasibility

I do not yet know whether a relatively simple purification process, without relying on expensive high-resolution chromatography, could achieve the purity required for human use.

I also need to understand the most realistic regulatory pathway in Bolivia and Latin America.

For example, the final product’s classification could have significant implications for manufacturing, quality control, clinical evidence, and approval requirements. I would need specialized regulatory guidance rather than assuming that a therapeutic peptide could be treated as an ordinary supplement.

What Would I Need to Do Next?

To determine whether this idea is technically and economically viable, I would prioritize three initial workstreams:

1. Expression and quantification: Produce and measure the first candidate variants.
2. Activity and stability: Evaluate whether the peptide retains the desired properties under relevant conditions.
3. Cost and regulatory assessment: Estimate purification costs and conduct a preliminary consultation regarding the regulatory pathway.

These steps would help transform the concept from an attractive biological hypothesis into an evidence-based engineering project.

Final Reflection

This project combines several areas I want to explore throughout HTBAA: biotechnology, computational design, automation, entrepreneurship, and public health.

My background in software and artificial intelligence has taught me to approach complex problems by breaking them into systems, testing assumptions, and iterating toward practical solutions.

I want to bring that mindset into biological engineering.

What interests me most is not simply producing a molecule. It is exploring whether we can design a manufacturing process that makes a potentially valuable biological tool more accessible to the people who need it.

The central question behind this project is:

Can we use accessible biomanufacturing technologies to expand the freedom and recovery options available to people affected by addiction?

That is the problem I would like to begin investigating.