Individual Final Project

Goal Demonstrate that you can apply HTGAA concepts (e.g., Benchling workflows, computational protein design) in a focused, well-documented project.

Timetable (work log)

To-do notes

• Keep this page in sync with your slides if the idea changes.

SECTION 1 — Abstract

Ischemia-reperfusion (I/R) injury, where blood supply restoration paradoxically worsens tissue damage, is a critical challenge in conditions like heart attacks and organ transplantation. This project focuses on addressing a specific mitochondrial disruption central to I/R injury: the Cyclophilin D (CypD)-mediated opening of the mitochondrial permeability transition pore (mPTP).

The significance lies in pioneering a targeted therapeutic, as no FDA-approved drugs currently address this precise mechanism. The broad objective is to first computationally design and then experimentally validate a peptide inhibitor of CypD. The central hypothesis is that a peptide, designed using computational tools to target a specific sequence on CypD, can prevent mPTP opening, thereby mitigating calcium overload, ATP depletion, and subsequent cell death.

The first specific aim (HTGAA focus) involves identifying the CypD target and computationally designing the therapeutic peptide, followed by initiating its synthesis and preliminary in vitro validation.

Subsequent aims (Master’s thesis) will involve broader in silico, in vitro (e.g., MTT assay), and in vivo evaluations of the peptide, with a long-term aim of progressing successful candidates through clinical trials to become an approved treatment for myocardial infarction and similar I/R-related conditions.

SECTION 2 — Project Aims

• Aim 1 (HTGAA scope): Identify a mitochondrial dysfunction implicated in I/R injury and computationally design a peptide-based therapeutic to address it. Use bioinformatics databases to select a target (e.g., Cyclophilin D and its role in mPTP opening) and protein-design tools (AI-assisted approaches) to generate a candidate inhibitory peptide sequence. Begin synthesis planning and initial in vitro validation (e.g., cloning into an expression vector such as pET-28a(+), expression in E. coli, and an initial cell-viability assay like MTT).
• Aim 2 (thesis scope): Perform comprehensive evaluation of the designed peptide and explore broader therapeutic pathways related to the targeted mitochondrial disruption—in silico docking/MD of peptide–CypD interaction; in vitro characterization (e.g., assays probing mPTP, ATP levels); progress to in vivo studies for therapeutic potential and safety.
• Aim 3 (impact & iteration): Define criteria to select top peptide candidates, iterate designs (e.g., point mutations, length/chemistry variants), and document decision points for potential translational follow-up.

Notes on tooling (search spaces)

When scouting tools and prior work, look across:

• Literature search portals (PubMed/Nature journals)
• GitHub (open-source repos, pipelines)
• Hugging Face (protein/antibody design models)
• Model families you tried/plan to try: AfDesign, EvoBind, BindCraft, RFdiffusion (record versions/seeds/params)

Deliverables (for this page)

• A clear abstract and three aims (updated as the project evolves)
• A timetable (work log)
• Links to slides and any relevant external resources
• Screenshots/figures you generate during design & evaluation (add as you go)