Targeted drugs associated with trimethylamine and/or trimeihylamine-n-oxide

1. A computer-implemented method for identifying at least one compound for treating a patient with a condition associated with at least one of trimethylamine (TMA), trimethylamine N-oxide (TMAO), or derivatives thereof, the method comprising:

determining, by one or more processors, a representative sequence of an enzyme associated with the at least one of TMA, TMAO, and derivatives thereof, wherein the representative sequence is representative of a set of sequences of the enzyme for at least one taxon from a set of microorganism taxa;

generating, by the one or more processors, a protein structure model of the enzyme based on the representative sequence of the enzyme;

determining, by the one or more processors, a control binding parameter to the enzyme based on a control docking simulation with the protein structure model and a control molecule;

determining, by the one or more processors, using a machine learning algorithm, a set of compound binding parameters to the enzyme based on a set of compound docking simulations with the protein structure model and a library of compounds; and

identifying, by the one or more processors, the at least one compound, from the library of compounds, for treating the patient with the condition associated with the at least one of TMA, TMAO, and derivatives thereof, based on a comparison between the control binding parameter and the set of compound binding parameters.

2. The method of claim 1 , wherein the enzyme comprises at least one of choline trimethylamine-lyase (CutC) enzyme or Rieske-type oxygenase (CntA) enzyme, and

wherein the at least one taxon comprises at least one of Firmicutes or Proteobacteria.

3. The method of claim 2 , wherein the at least one compound comprises at least one of Methyl 4-methyl-4-piperidinecarboxylate; Methyl heptanoate; 3-Methylpyridazine; 4,5-Dimethyl-1,2-oxazol-3-amine; 2-(2-Hydroxyethoxy)phenol; 2-Hydroxy-N-(3-pyridinylmethyl)ethanaminium; 3-Phenyl-1-propanol; (2R)-6-Methyl-2-heptanol; 2-Phenoxyacetohydrazide; N-Hydroxyoctanamid; Cyclobutanecarbohydrazide; Phenylhydrazine; (1S,4R)-2-Azabicyclo[2.2.1]hept-5-en-3-one; salicylamide; Adamantane; 3-Azabicyclo[3.3.1]nonane; N-Hydroxy-2-methylbenzenecarboximidamide; (−)-camphene; (1S,2S,4S)-Bicyclo[2.2.1]hept-5-en-2-ylmethanol; Dicyclopentadiene; (8-anti)-3-Azabicyclo[3.2.1]octan-8-ol; (1R,2S,6R,7S)-Tricyclo[5.2.1.02,6]deca-3,8-diene; pharmaceutically acceptable forms thereof; or salts thereof.

4. The method of claim 3 , wherein the condition comprises at least one of a cardiovascular condition, a renal condition, a metabolic-related condition, or a nutrition-related condition.

5. The method of claim 2 , wherein the at least one compound comprises at least one of 2-Ethyl-1-butanol; (2R)-3,3-Dimethyl-1,2-butanediol; (2S)-3,3-Dimethyl-1,2-butanediol; (2S)-4-Methyl-2-pentanol; (2S)-3-Methyl-2-butanol; (2R)-4-Methyl-2-pentanol; (2R)-3-Methyl-2-butanol; (2S)-2-Pentanol; (2S)-2-Methyl-1,4-butanediol; 2-Methyl-2,4-butanediol; Trimethylolpropane; pharmaceutically acceptable forms thereof; or salts thereof.

6. The method of claim 2 , wherein the at least one compound comprises at least one of 3-(4-Methoxyphenyl)propanal; 1-(3-Pyridinyl)-2-propanamine; 2-[(2R)-2-Butanyl]phenol; 4-Propylbenzoic acid; (2S)-1-(Benzyloxy)-2-propanol; Methyl 3-(4-hydroxyphenyl)propanoate; α-Methylphenyl alanine; 2,2-Dimethyl-1-phenyl-1-propanol; Methyl (2R)-hydroxy(phenyl)acetate; (2S)-2-Phenylpyrrolidinium; 4-Methyl-3-phenyl-1,2-oxazol-5-amine; 4,4′-Biphenyldiamine; 4′-Methyl-2 biphenylcarbonitrile; 4-Biphenylol; 2-[3-(4-Methylphenyl)-1,2-oxazol-5-yl]thanol; 4-Biphenylcarboxamide; 4-Ethynylbiphenyl; 5-(4-Methylphenyl)-1H-1,2,4-triazol-3-amine; 5-(4-Methylphenyl)-1H-pyrazol-3-amine; 4-Hydroxycatechol; 3-Phenyl-1H-pyrazole-5-carbohydrazide; 4-Methyl-1,3-benzenediol; pharmaceutically acceptable forms thereof; or salts thereof.

7. The method of claim 2 , wherein the at least one compound comprises at least one of N-(2-Hydroxyethyl)-1,3-propanediaminium; 3-Methoxy-3-methylbutanol; 4-Pyridinylmethanaminium; N-Methyl-3-pyridinamine; 2-Methoxypyridine; 5-Methyl-3-pyridinamine; 1-(4-Methyl-3-pyridinyl)methanamine; Mesitylene; (E)-Benzaldoxime′ (3R)-2,2,4-Trimethyl-1,3-pentanediol; (1R,4R)-2-Azabicyclo[2.2.1]hept-2-ylacetic acid; 3-ACETYLPHENOL; 3-Hydroxybenzoicacid; 1H-Indol-7-ylmethanol; 3-Vinylaniline; (3s,5s,7s)-1-Isocyanatoadamantane; (1R,2S,5R)-2-Hydroxy-2,6,6-trimethylbicyclo[3.1.1]heptan-3-one; (−)β-Pinene; 2H-Isoindole-1,3-diamine; (3s,5s,7s)-1-Adamantanol; (3-Aminobicyclo[2.2.1]hept-2-yl)methanol; 3-(Hydrazinomethyl)phenol; (1S,2R)-2-Carbamoylcyclohexanaminium; (1S,4R)-1,3,3-Trimethylbicyclo[2.2.1]heptan-2-one; (1R,4S)-1,3,3-Trimethylbicyclo[2.2.1]heptan-2-one; pharmaceutically acceptable forms thereof; or salts thereof.

8. The method of claim 2 , wherein the at least one compound comprises at least one of N-Methylglutamic acid; 4-(1-Pyrrolidinyl)butanoic acid; 4-Methyl-4-piperidinecarboxylic acid; Isonipecotic acid; pharmaceutically acceptable forms thereof; or salts thereof.

9. The method of claim 2 , wherein the at least one compound comprises at least one of N-propylbenzene; N-Ethyl-2-pyridinamine; (4R)-4-Amino-1-propyl-2-pyrrolidinone; 2,5-Diaminotoluene; Ethyl phenyl ether; Phenylcyanate; 1-(2-Cyclopenten-1-yl)acetone; 2-Amino-3-methylpyridinium; E-pyridine-3-aldoxime; N-Cyclohexylformamide; 2-Methyl-2-hexenoic acid; 4-Heptanaminium; pharmaceutically acceptable forms thereof; or salts thereof.

10. The method of claim 2 , wherein the at least one compound comprises at least one of 3,4-Anhydro-3-carboxy-2-deoxy-L-threo-pentaric acid; 2,2′-[(2-Hydroxyethyl)imino]diacetic acid; 1H-Tetrazol-5-ylacetic acid; Diacetylacetone; (2S)-2-Acetoxypropanoic acid; pharmaceutically acceptable forms thereof; or salts thereof.

11. The method of claim 2 , wherein the at least one compound comprises at least one of 4,4′-Biphthalic anhydride; Bis(1H-benzotriazol-1-yl)methanone; 2-Anthraquinonesulfonic acid; 3-(1,3-Dioxo-1,3-dihydro-2H-isoindol-2-yl)benzonitrile; 2-phenylquinazolin-4-ol; 4-Amino-2-(1,3-benzothiazol-2-yl)phenol; 4-Phenyl-1(2H)-phthalazinone; Benzodioxol-5-yl)-2-methyl-3-furoic acid; (5R)-5-(2-Naphthyl)dihydro-2(3H)-furanone; 3-[5-(3-Methylphenyl)-1,3,4-oxadiazol-2-yl]propanoic acid; 9-ETHYNYLPHENANTHRENE; PHA-767491; 3-Amino-2-methylphenol; 5-(4-Methylphenyl)-2-furoic acid; 8-Methyl-4H-thieno[3,2-c]chromene-2-carboxylic acid; resorcinol monobenzoate; 3-Methoxy-4-biphenylcarbaldehyde; (7-Amino-4-methyl-2-oxo-2H-chromen-3-yl)acetic acid; 2,3-Dihydro-1H-inden-5-yl(oxo)acetic acid; 3-(2-Pyridyl)aniline; 4-(3-Methyl-1H-1,2,4-triazol-5-yl)aniline; Benzidine; (DL)-3-O-Methyldopa; Methyl (2E)-3-(2-amino-5-methyl-3-pyridinyl)acrylate; (5-Methylfuro[2,3-b]pyridin-2-yl)methanol; (2R)-2,3-Dihydro-1,4-benzodioxin-2-ylmethanaminium; R-phenylethyl propionate; i-propyl benzoate; 4-Acetotoluide; (1S)-1-(2,5-Dimethylphenyl)ethanaminium; (1R)-2-Methyl-2,5-cyclohexadiene-1-carboxylic acid; (2,2-Dimethoxyethyl)benzene; pharmaceutically acceptable forms thereof; or salts thereof.