Peptidomimetic Compound Design for Precise Low-Energy Structures

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Solution Overview

Problem

There are few successful developments of peptidomimetics due to the lack of effective methods for designing compounds with desired structures.

Innovation Solution

A method involving a computer-generated molecular formula, random molecule generation using an adjacency matrix, and selection based on predefined conditions to create a peptidomimetic backbone with specific structural and energetic criteria, including cage-like carbon backbones and amino acid-like structures.

Engineering Contradictions & Design Principles

VSEngineering Contradiction Analysis

1Manufacturing precision

If conventional methods are used for peptidomimetic design, then the design process is simple, but the structural precision and success rate are low

Engineering Contradiction:

Improvestructural precisionVSAvoiddesign complexity

Core Design Contradiction:

Manufacturing precisionVSDevice complexity

Solution Approach 1:

The patent replaces conventional manual or simple computational design methods with an AI-based computational system that uses adjacency matrices and machine learning algorithms to generate and evaluate molecular structures, thereby achieving higher structural precision through automated intelligent systems

Inventive Principle:

Principle #28Mechanics substitution (Replace mechanical system)

Solution Approach 2:

The patent systematically varies molecular parameters such as ring size (5- or 6-membered rings), bond types (single, double, triple bonds), and atomic compositions (C, H, O, N, S) to explore the chemical space and identify optimal peptidomimetic structures that satisfy predefined conditions

Inventive Principle:

Principle #35Parameter changes

2Adaptability or versatility

If random molecule generation is used, then structural diversity is achieved, but the energy optimization is insufficient

Engineering Contradiction:

Improvestructural diversityVSAvoidenergy optimization

Core Design Contradiction:

Adaptability or versatilityVSUse of energy by moving object

Solution Approach 1:

The patent implements a feedback mechanism where generated molecular structures are evaluated against predefined conditions including energy thresholds (MMFF energy ≤150 kcal/mol), and the AI system iteratively refines the generation process based on this feedback to simultaneously achieve structural diversity and energy optimization

Inventive Principle:

Principle #23Feedback

Solution Approach 2:

The patent performs preliminary filtering of generated molecules by checking against structural conditions (ring sizes, bond types, atomic compositions) before full energy evaluation, thereby efficiently narrowing down the search space to structurally viable candidates that also meet energy criteria

Inventive Principle:

Principle #10Preliminary action

Data Source

PatentUS20250304616A1Novel peptidomimetic compound and design

Publication Date: 2025.10.02 IRIMAJIRI THERAPEUTICS INC

AI summary

The present disclosure provides a design and synthesis of a useful carbon skeleton, a design and synthesis of a peptidomimetic molecule and applications and uses based thereon. More particularly, provided is a method for designing a compound skeleton with a desired structure, said method comprising, with the use of a computer: (1) a step for generating a molecular formula of a carbon-containing compound; (2) a step for randomly synthesizing molecules using the adjacency matrix and extracting compounds that correspond to the molecular formula among the randomly synthesized molecules; and (3) a step for selecting a compound that satisfies preset conditions.