Timetable

To-do list:

SECTION 1: ABSTRACT

1. Provide an abstract/summary for your project. (minimum 150 words)

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 visionary aim of progressing successful candidates through clinical trials to become an approved treatment for myocardial infarction and similar I/R-related conditions.

See an example abstract here!

SECTION 2: PROJECT AIMS

2. Outline three aims of your final project (min. 3 sentences, at least one for each aim)

• The first aim of my final project is to identify a mitochondrial dysfunction implicated in ischemia-reperfusion injury and computationally design a peptide-based therapeutic to address it by utilizing bioinformatics databases to select a target (e.g., Cyclophilin D and its role in mPTP opening) and protein design tools (e.g., AI-driven approaches as suggested by "AI Design" in project materials, slide 2) to generate a candidate inhibitory peptide sequence (e.g., the provided sequence SSDEPSKDSMSKKSSKSPAGNQAGQVNNPDASKRETSKSSHFENPASSCTHQETHWEFCERMKKYEKERF, slide 2). This design work will be the focus of the HTGAA project, with subsequent synthesis of the designed peptide gene (e.g., via Twist Bioscience) and initiation of preliminary in vitro validation, such as cloning into an expression vector (e.g., pET-28a(+), slide 2), E. coli expression, and an initial cell viability assay (e.g., MTT assay, slide 2).
• The second aim, envisioned as part of my Master's thesis, is to conduct a comprehensive evaluation of the designed peptide and explore broader therapeutic pathways related to the targeted mitochondrial disruption. This will involve extensive in silico modeling (e.g., molecular docking, dynamics simulations of the peptide-CypD interaction), in vitro characterization of the peptide's efficacy and mechanism of action using cell-based assays (like the MTT cytotoxicity assay mentioned on slide 2, and potentially others exploring mPTP opening directly or ATP synthesis levels), and progressing to in vivo studies in animal models of ischemia-reperfusion injury to assess its therapeutic potential and safety.