US 12,437,846 B2
Identifying drivers of molecule toxicity using toxicity analysis trees
Brandon White, San Francisco, CA (US); Alexander Bremner Upjohn Beatson, San Francisco, CA (US); Katherine Lynn Titterton, San Francisco, CA (US); Daniil Boiko, San Francisco, CA (US); Ángel Alexander Cabrera, San Francisco, CA (US); and Alex Tim Bäuerle, San Francisco, CA (US)
Assigned to AXIOMBIO, INC., San Francisco, CA (US)
Filed by AXIOMBIO, INC., San Francisco, CA (US)
Filed on Jan. 3, 2025, as Appl. No. 19/009,903.
Claims priority of provisional application 63/651,057, filed on May 23, 2024.
Claims priority of provisional application 63/563,254, filed on Mar. 8, 2024.
Prior Publication US 2025/0285715 A1, Sep. 11, 2025
Int. Cl. G16C 20/30 (2019.01); G16C 20/50 (2019.01); G16C 20/70 (2019.01); G16C 20/80 (2019.01)
CPC G16C 20/30 (2019.02) [G16C 20/50 (2019.02); G16C 20/70 (2019.02); G16C 20/80 (2019.02)] 20 Claims
OG exemplary drawing
 
1. A method comprising:
performing, by one or more computers, operations comprising:
obtaining data identifying an input molecule;
generating data defining a toxicity analysis tree for the input molecule, wherein:
each node in the toxicity analysis tree represents a respective molecule and is associated with data defining a toxicity prediction for the molecule represented by the node;
a root node of the toxicity analysis tree represents the input molecule; and
each child node of the toxicity analysis tree represents a child molecule that is generated by modifying a parent molecule represented by a parent node of the child node;
wherein generating the toxicity analysis tree comprises iteratively expanding the toxicity analysis tree over a plurality of iterations, comprising, at each of one or more iterations:
selecting a node in the toxicity analysis tree for expansion at the iteration based at least in part on the toxicity predictions for the nodes in the toxicity analysis tree;
generating data defining a modified molecule by modifying a molecule represented by the selected node;
determining a toxicity prediction for the modified molecule; and
expanding the toxicity analysis tree by: (i) adding a new node representing the modified molecule to the toxicity analysis tree as a child node of the selected node, and (ii) associating the new node with the toxicity prediction for the modified molecule; and
processing the toxicity analysis tree to generate a respective toxicity score for each of a plurality of molecule fragments in the input molecule that characterizes an impact of the molecule fragment on a toxicity of the input molecule;
determining a modified molecule having a lower predicted toxicity than the input molecule by modifying the input molecule based at least in part on the toxicity scores for the plurality of molecule fragments in the input molecule; and
selecting the modified molecule for physical synthesis; and
after performing the operations by the one or more computers to select the modified molecule for physical synthesis:
physically synthesizing the modified molecule selected for physical synthesis.