Table 1.
MolDock docking energies of co-crystallized ligands and root mean squared deviations between the co-crystallized ligand and the re-docked poses of the co-crystallized ligand with Trichomonas vaginalis and homologous human protein structures.
| Protein | PDB code | Co-crystallized ligand | Edock (kJ/mol) | RMSD (Å) |
|---|---|---|---|---|
| TvMGL | 1E5E | N-(Hydroxy{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)norvaline | -127.6 | 1.13 |
| 1E5F | Pyridoxal-5′-phosphate | -69.4 | 0.57 | |
| TvCPCAC1 | [1FH0] a | N-α-[(4-Methylpiperazin-1-yl)carbonyl]-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-l-phenylalaninamide | -132.6 | 2.69 |
| TvCP2 | [2F7D] | (1R,2R)-N-(2-Aminoethyl)-2-{[(4-methoxyphenyl)sulfonyl]methyl}-cyclohexanecarboxamide | -97.7 | 1.22 |
| TvPNP | 1Z34 | 2-Fluoro-2′-deoxyadenosine | -97.1 | 0.91 |
| 1Z36 | (1S)-1-(7-Amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-d-ribitol | -97.7 | 0.21 | |
| 2ISC | (3R,4R)-1-[(4-Amino-5H-pyrrolo [3,2-d]pyrimidin-7-yl),ethyl]-4-(hydroxymethyl)pyrrolidin-3-ol | -104.0 | 0.57 | |
| HsCatK | 1MEM | N-{(1R)-3-Phenyl-1-[2-(phenylsulfonyl)ethyl]propyl}-N-2-(piperazin-1-ylcarbonyl)-l-leucinamide | -136.2 | 2.74 |
| 1U9V | 6-(Cyclohexylamino)-9-[2-(4-methylpiperazin-1-yl)-ethyl]-9H-purine-2-carbonitrile | -41.7 | 4.03 | |
| HsCatL | 3HWN | N-α-[(3-t-Butyl-1-methyl-1H-pyrazol-5-yl)carbonyl]-N-[(2E)-2-iminoethyl]-3-{5-[(Z)-iminomethyl]-1,3,4-oxadiazol-2-yl}-l-phenylalaninamide | -135.1 | 6.65 |
| 3OF8 | N-α-[(Benzyloxy)carbonyl]-N-[(2S)-1-(4-t-butoxyphenyl)-4-hydroxy-3-oxobutan-2-yl]-l-phenylalaninamide | -120.7 | 6.43 | |
| HsPNP | 3BGS | 3-Hydroxy-4-hydroxymethyl-1-(4-oxo-4,4a,5,7a-tetrahydro-3H-pyrrolo[3,2-d]pyrimidin-7-ylmethyl)-pyrrolidinium | -102.8 | 2.93 |
| 3INY | 7-Deazaguanine | -74.0 | 0.61 |
a PDB codes in brackets are Trichomonas vaginalis homology models based on that protein structure. TvMGL, T. vaginalis methionine gamma-lyase; TvCPCAC1, T. vaginalis cathepsin L-like protease; TvCP2, T. vaginalis papain-like cysteine protease C2; TvPNP, T. vaginalis purine nucleoside phosphorylase; HsCatK, human cathepsin K; HsCatL, human cathepsin L; HsPNP, human purine nucleoside phosphorylase.