Bioisosteric Fragment Replacement for Lower-Toxicity Molecules
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Solution Overview
Problem
Conventional methods for determining molecule toxicity require physical synthesis and testing, consuming significant resources and time, and lack comprehensive characterization of toxicity dimensions.
Innovation Solution
A system utilizing machine learning models to predict molecule toxicity through a toxicity prediction model, generating toxicity dose-response curves without physical synthesis, and analyzing molecule fragments to identify contributors and generate bioisosteric replacements.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If physical synthesis and testing methods are used to determine molecule toxicity, then comprehensive toxicity characterization can be achieved, but significant resources and time are consumed
Solution Approach 1:
The patent applies preliminary action by using machine learning models to predict toxicity outcomes before physical synthesis and testing are performed. The system processes molecular structures through trained ML models to generate toxicity predictions, enabling early filtering of problematic compounds and reducing the number of physical experiments needed, thus saving time while maintaining comprehensive toxicity characterization.
2Measurement precision
If physical synthesis and testing methods are used to determine molecule toxicity, then accurate toxicity data can be obtained, but significant computational and physical resources are consumed
Solution Approach 1:
The patent applies copying by creating virtual representations of molecular toxicity through machine learning models instead of performing physical synthesis and testing. The ML models are trained on existing toxicity data and then used to generate predictions for new molecules, effectively copying the information-gathering process in silico rather than in vitro, thereby reducing resource consumption while maintaining data accuracy.
3Use of energy by moving object
If machine learning models are used to predict molecule toxicity, then resource consumption is reduced, but comprehensive characterization of all toxicity dimensions may be limited
Solution Approach 1:
The patent applies universality by designing a multi-functional machine learning system that predicts multiple toxicity dimensions simultaneously using a single model framework. The system processes molecular structures through various ML models that output predictions for different toxicity endpoints, enabling comprehensive toxicity characterization across multiple dimensions while consuming fewer resources than separate physical assays for each endpoint.
4Reliability
If conventional toxicity testing methods are used, then thorough toxicity assessment can be performed, but the drug development process is slowed down
Solution Approach 1:
The patent applies preliminary action by performing toxicity assessments early in the drug discovery process using machine learning predictions before committing to costly and time-consuming physical synthesis and testing. This early filtering maintains thorough toxicity assessment through comprehensive ML modeling while accelerating drug development speed by identifying problematic compounds before they advance to later stages.
Data Source
AI summary
Methods, systems, and apparatus, including computer programs encoded on a computer storage medium, for predicting toxicity of molecules. In one aspect, a method comprises: obtaining data identifying: (i) an input molecule, and (ii) a target molecule fragment; determining, for each candidate molecule fragment in a database of candidate molecule fragments, a respective similarity measure between: (i) an embedding of the target molecule fragment, and (ii) an embedding of the candidate molecule fragment; selecting a plurality of candidate molecule fragments for inclusion in a set of alternative molecule fragments based on the similarity measures; and generating data defining a plurality of modified molecules, wherein each modified molecule is a modified version of the input molecule where the target molecule fragment is replaced by a respective alternative molecule fragment from the set of alternative molecule fragments; and generating a respective toxicity prediction for each of the plurality of modified molecules.


