Miniaturized Shank3 Protein Design for AAV Delivery

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Solution Overview

Problem

Current treatments for autism spectrum disorder (ASD) and intellectual disability associated with Shank3 mutations are ineffective, and existing methods struggle to restore Shank3 protein function due to its large size exceeding the packaging capacity of AAV vectors.

Innovation Solution

Development of miniaturized Shank3 proteins (MiniShank3) encoded by non-naturally occurring polynucleotides, which are delivered via AAV vectors to restore Shank3 activity in brain cells, utilizing specific domains that are critical for protein function while removing non-essential regions to fit within the vector capacity.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Reliability

If full-length Shank3 protein is used for gene therapy, then complete protein function is achieved, but the protein size exceeds AAV vector packaging capacity

Engineering Contradiction:

Improveprotein functionVSAvoidprotein size

Core Design Contradiction:

ReliabilityVSLength of moving object

Solution Approach 1:

The Shank3 protein is divided into essential functional domains (SH3, PDZ, Homer binding, Cortactin binding, and SAM domains) that are retained in the miniaturized version, while non-essential regions are removed. This segmentation allows the protein to fit within AAV packaging capacity while preserving critical synaptic scaffolding functions.

Inventive Principle:

Principle #1Segmentation

Solution Approach 2:

Non-essential regions of the Shank3 protein sequence are extracted and removed to create a miniaturized version. The extracted essential domains are then reassembled to form a functional mini-Shank3 protein that fits within the AAV vector packaging limit of approximately 4.7 kb.

Inventive Principle:

Principle #2Taking out (Extraction)

2Length of moving object

If miniaturized Shank3 protein is used, then AAV vector packaging capacity is respected, but complete protein function may be compromised

Engineering Contradiction:

Improveprotein sizeVSAvoidprotein function

Core Design Contradiction:

Length of moving objectVSReliability

Solution Approach 1:

Different regions of the Shank3 protein are treated differently: essential functional domains (SH3, PDZ, Homer binding, Cortactin binding, and SAM domains) are preserved with high fidelity, while non-essential regions are removed. This local quality approach ensures that critical protein-protein interactions at synapses are maintained while reducing overall size.

Inventive Principle:

Principle #3Local quality

Solution Approach 2:

The protein sequence parameters are modified by removing non-essential amino acid sequences while maintaining the structural and functional parameters of critical domains. This allows the protein to meet the size constraint (fitting within AAV packaging capacity) while preserving functional parameters such as binding affinity and scaffolding capability.

Inventive Principle:

Principle #35Parameter changes

Data Source

PatentUS20230340041A1Shank3 gene therapy approaches

Publication Date: 2023.10.26 MASSACHUSETTS INST OF TECH

AI summary

Aspects of the disclosure relate to non-naturally occurring polynucleotides encoding a Shank3 protein, AAV vectors comprising the polynucleotides, and gene therapy methods.