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Literature summary for 2.3.2.12 extracted from
- Discovery of small-molecule inhibitors targeting the ribosomal peptidyl transferase center (PTC) of M. tuberculosis (2019), Chem. Sci., 10, 8764-8767 .
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC19595411 | Mycobacterium tuberculosis |  |
| 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC19595411 | Mycolicibacterium smegmatis | |
| 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC19595411 | Staphylococcus aureus | |
| 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC22812775 | Mycobacterium tuberculosis | |
| 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC22812775 | Mycolicibacterium smegmatis | |
| 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine | i.e. ZINC22812775 | Staphylococcus aureus | |
| chloramphenicol | - |
Mycolicibacterium smegmatis | |
| eperezolid | ZINC03813328 | Mycobacterium tuberculosis | |
| eperezolid | ZINC03813328 | Mycolicibacterium smegmatis | |
| eperezolid | ZINC03813328 | Staphylococcus aureus | |
| linezolid | ZINC02008866 | Mycobacterium tuberculosis | |
| linezolid | ZINC02008866 | Mycolicibacterium smegmatis | |
| linezolid | ZINC02008866 | Staphylococcus aureus | |
| additional information | improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, docking study, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC | Mycobacterium tuberculosis | |
| additional information | improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC | Mycolicibacterium smegmatis | |
| additional information | improved small molecule inhibitors of the Mtb ribosomal PTC are obtained using a combination of NMR transverse relaxation times (T2) and computational chemistry approaches, inhibitor design from scaffolds, docking study, overview. Two phenylthiazole derivatives with low IC50 values are predicted by machine learning models as effective inhibitors. Screening of the ZINC database. Molecular docking of Mycobacterium tuberculosis-homologous Staphylococcus aureus peptidyl transferase center (PTC). Predicted binding of oxazolidinone antibiotics that target the ribosomal PTC | Staphylococcus aureus | |
| posizolid | ZINC03982517 | Mycobacterium tuberculosis | |
| posizolid | ZINC03982517 | Mycolicibacterium smegmatis | |
| posizolid | ZINC03982517 | Staphylococcus aureus | |
| radezolid | ZINC40379938 | Mycobacterium tuberculosis | |
| radezolid | ZINC40379938 | Mycolicibacterium smegmatis | |
| radezolid | ZINC40379938 | Staphylococcus aureus | |
| sutezolid | ZINC03810825 | Mycobacterium tuberculosis | |
| sutezolid | ZINC03810825 | Mycolicibacterium smegmatis | |
| sutezolid | ZINC03810825 | Staphylococcus aureus | |
| tedizolid | ZINC43100953 | Mycobacterium tuberculosis | |
| tedizolid | ZINC43100953 | Mycolicibacterium smegmatis | |
| tedizolid | ZINC43100953 | Staphylococcus aureus | |
| ZINC19944344 | - |
Mycobacterium tuberculosis | |
| ZINC19944344 | low inhibition | Mycolicibacterium smegmatis | |
| ZINC19944344 | - |
Staphylococcus aureus | |
| ZINC35154793 | - |
Mycobacterium tuberculosis | |
| ZINC35154793 | - |
Mycolicibacterium smegmatis | |
| ZINC35154793 | - |
Staphylococcus aureus | |
| ZINC37712815 | - |
Mycobacterium tuberculosis | |
| ZINC37712815 | low inhibition | Mycolicibacterium smegmatis | |
| ZINC37712815 | - |
Staphylococcus aureus | |
| ZINC37713642 | - |
Mycobacterium tuberculosis | |
| ZINC37713642 | - |
Mycolicibacterium smegmatis | |
| ZINC37713642 | - |
Staphylococcus aureus | |
| ZINC37715345 | - |
Mycobacterium tuberculosis | |
| ZINC37715345 | - |
Mycolicibacterium smegmatis | |
| ZINC37715345 | - |
Staphylococcus aureus | |
| ZINC54418966 | - |
Mycobacterium tuberculosis | |
| ZINC54418966 | - |
Mycolicibacterium smegmatis | |
| ZINC54418966 | - |
Staphylococcus aureus | |
| ZINC71794395 | - |
Mycobacterium tuberculosis | |
| ZINC71794395 | - |
Mycolicibacterium smegmatis | |
| ZINC71794395 | - |
Staphylococcus aureus | |
| ZINC90290472 | - |
Mycobacterium tuberculosis | |
| ZINC90290472 | low inhibition | Mycolicibacterium smegmatis | |
| ZINC90290472 | - |
Staphylococcus aureus | |
Localization
| Localization | Comment | Organism | GeneOntology No. | Textmining |
|---|---|---|---|---|
| ribosome | - |
Staphylococcus aureus | 5840 | - |
| ribosome | - |
Mycolicibacterium smegmatis | 5840 | - |
| ribosome | - |
Mycobacterium tuberculosis | 5840 | - |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Mycolicibacterium smegmatis | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Staphylococcus aureus | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycolicibacterium smegmatis | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycobacterium tuberculosis | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycobacterium tuberculosis ATCC 27294 | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycolicibacterium smegmatis ATCC 700084 | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycobacterium tuberculosis H37Rv | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | Mycolicibacterium smegmatis mc(2)155 | - |
tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Mycobacterium tuberculosis | - |
- |
- |
| Mycobacterium tuberculosis ATCC 27294 | - |
- |
- |
| Mycobacterium tuberculosis H37Rv | - |
- |
- |
| Mycolicibacterium smegmatis | - |
i.e. Mycobacterium smegmatis | - |
| Mycolicibacterium smegmatis ATCC 700084 | - |
i.e. Mycobacterium smegmatis | - |
| Mycolicibacterium smegmatis mc(2)155 | - |
i.e. Mycobacterium smegmatis | - |
| Staphylococcus aureus | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Staphylococcus aureus | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycolicibacterium smegmatis | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycobacterium tuberculosis | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycobacterium tuberculosis ATCC 27294 | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycolicibacterium smegmatis ATCC 700084 | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycobacterium tuberculosis H37Rv | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
| peptidyl-tRNA1 + aminoacyl-tRNA2 | - |
Mycolicibacterium smegmatis mc(2)155 | tRNA1 + peptidyl(aminoacyl-tRNA2) | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| MSMEI_5283 | locus name | Mycolicibacterium smegmatis |
| peptidyl transferase center | - |
Staphylococcus aureus |
| peptidyl transferase center | - |
Mycolicibacterium smegmatis |
| peptidyl transferase center | - |
Mycobacterium tuberculosis |
| PTC | - |
Staphylococcus aureus |
| PTC | - |
Mycolicibacterium smegmatis |
| PTC | - |
Mycobacterium tuberculosis |
Temperature Optimum [°C]
| Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
|---|---|---|---|
| 37 | - |
assay at | Staphylococcus aureus |
| 37 | - |
assay at | Mycolicibacterium smegmatis |
| 37 | - |
assay at | Mycobacterium tuberculosis |
pH Optimum
| pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
|---|---|---|---|
| 7.5 | - |
assay at | Staphylococcus aureus |
| 7.5 | - |
assay at | Mycolicibacterium smegmatis |
| 7.5 | - |
assay at | Mycobacterium tuberculosis |
IC50 Value
| IC50 Value | IC50 Value Maximum | Comment | Organism | Inhibitor | Structure |
|---|---|---|---|---|---|
| 0.0028 | - |
pH 7.5, 37°C | Mycolicibacterium smegmatis | 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine | |
| 0.0071 | - |
pH 7.5, 37°C | Mycolicibacterium smegmatis | chloramphenicol | |
| 0.0091 | - |
pH 7.5, 37°C | Mycolicibacterium smegmatis | 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | for the ribosomal PTC used (U2673-C2836), there is 100% identity between Mycobacterium tuberculosis and Mycobacterium smegmatis. The Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC | Mycobacterium tuberculosis |
| evolution | the Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC | Staphylococcus aureus |
| additional information | the enzyme is part of the peptidyl transferase center (PTC) | Staphylococcus aureus |
| additional information | the enzyme is part of the peptidyl transferase center (PTC) | Mycolicibacterium smegmatis |
| additional information | the enzyme is part of the peptidyl transferase center (PTC) | Mycobacterium tuberculosis |
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Release 2023.1 (January 2023)
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