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公开(公告)号：US20230120018A1
公开(公告)日：2023-04-20
申请号：US18058110
申请日：2022-11-22
申请人： Genentech, Inc.
摘要： The present disclosure relates to polypeptide degradation, and in particular to techniques for predicting the likelihood that a peptide bond for a given polypeptide molecule is susceptible to a cleavage reaction. Particularly, aspects of the present disclosure are directed to generating a representation of a polypeptide, performing a molecular-dynamics simulation using the representation to obtain a set of polypeptide conformations, determining, for each polypeptide conformation, a spatial characteristic of an amino acid, estimating a nucleophilic attack distance of each polypeptide conformation based on the spatial characteristic, identifying a reactive conformation that is susceptible to a cleavage reaction based on the nucleophilic attack distance of each polypeptide conformation, determining a free energy of the spatial characteristic of the amino acid in the reactive conformation; and predicting a probability of the side chain of the amino acid being trapped in the reactive conformation based on the free energy.
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公开(公告)号：US20220208309A1
公开(公告)日：2022-06-30
申请号：US17587760
申请日：2022-01-28
申请人： Genentech, Inc.
摘要： The present disclosure relates to polypeptide therapeutics, and in particular to techniques for predicting side-chain degradation in polymers through physics based simulations. Particularly, aspects of the present disclosure are directed to generating a representation of a polymer having one or more side chains, performing a molecular-dynamics simulation using the representation to obtain a set of polymer conformations, determining, for each polymer conformation, one or more spatial characteristics of the polymer while in the polymer conformation, identifying, based on the one or more spatial characteristics, an incomplete subset of the set of polymer conformations estimated to undergo one or more reactions of a particular type, and estimating, based on a size of the incomplete subset, a probability of a reaction in which the polymer is a reactant and a particular other molecule is a product.
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