Abstract: Therapeutic compositions and an associated method for improving a Toll-like receptor (TLR)-related condition, including determining a set of peptide sequences associated with a microorganism-related modulator of a TLR, determining a first set of binding parameters for the set of peptide sequences in relation to the TLR, selecting a target subset of peptide sequences from the set of peptide sequences based on the first set of binding parameters, reengineering the target subset of peptide sequences based on mutating amino acid residues of the target subset of peptide sequences, determining a second set of binding parameters for the reengineered target subset of peptide sequences in relation to the TLR, and identifying a first peptide for use in a therapeutic composition for improving the TLR-related condition, based on the second set of binding parameters for the reengineered target subset of peptide sequences.

Abstract: Embodiments of a method and/or system can include administering, to a patient with one or more conditions associated with at least one of TMA, TMAO, and/or derivatives thereof, a therapeutically effective amount of a compound for affecting inhibiting one or more CutC enzymes and/or CntA enzymes associated with microorganisms from at least one taxon from a set of microorganism taxa.

Abstract: The present disclosure relates to pharmaceutical compounds and compositions and methods for treating an allergy and Crohn's disease. Methods for treating an allergy can include (a) predicting potential epitopes based proteomes of microbiome and that of an allergen, (b) filtering the potential epitopes obtained in step a) to result in a list of epitopes; and (c) reengineering the list of epitopes obtained in step b) to result in the new epitope. Methods for treating Crohn's disease can include (a), identifying one or more binding regions of an HLA class II protein and/or hemagglutinin to I2 superantigen; (b) determining a first peptide sequence corresponding to the one or more binding regions, and (c) producing a peptide inhibitor having a second peptide sequence that is a mutation of the first peptide sequence, wherein the second peptide sequence has a stronger binding affinity to the I2 superantigen than the first peptide sequence.

Abstract: Embodiments of a method and/or system can include administering, to a patient with one or more conditions associated with at least one of TMA, TMAO, and/or derivatives thereof, a therapeutically effective amount of a compound for affecting inhibiting one or more CutC enzymes and/or CntA enzymes associated with microorganisms from at least one taxon from a set of microorganism taxa.

Abstract: Embodiments of a method and/or system (e.g, for metabolism-related prediction) can include: generating an enzyme dataset; generating a substrate dataset; generating a metabolism model such as for predicting an enzyme feature associated with metabolism of a query molecule, based on the enzyme dataset and/or the substrate dataset; determining a microorganism taxon (and/or microorganism taxa) S140 associated with the metabolism of the query molecule based on one or more predicted enzyme features of the metabolism model (e.g., machine learning model; etc.) and/or determining a query molecule score (e.g., drug score) for one or more users based on the microorganism taxon.

Abstract: Embodiments of a method and/or system can include administering, to a patient with one or more conditions associated with at least one of TMA, TMAO, and/or derivatives thereof, a therapeutically effective amount of a compound for affecting inhibiting one or more CutC enzymes and/or CntA enzymes associated with microorganisms from at least one taxon from a set of microorganism taxa.

Abstract: Therapeutic compositions and an associated method for improving a Toll-like receptor (TLR)-related condition, including determining a set of peptide sequences associated with a microorganism-related modulator of a TLR, determining a first set of binding parameters for the set of peptide sequences in relation to the TLR, selecting a target subset of peptide sequences from the set of peptide sequences based on the first set of binding parameters, reengineering the target subset of peptide sequences based on mutating amino acid residues of the target subset of peptide sequences, determining a second set of binding parameters for the reengineered target subset of peptide sequences in relation to the TLR, and identifying a first peptide for use in a therapeutic composition for improving the TLR-related condition, based on the second set of binding parameters for the reengineered target subset of peptide sequences.