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Literature summary extracted from

  • Tam, B.; Sherf, D.; Cohen, S.; Eisdorfer, S.A.; Perez, M.; Soffer, A.; Vilenchik, D.; Akabayov, S.R.; Wagner, G.; Akabayov, B.
    Discovery of small-molecule inhibitors targeting the ribosomal peptidyl transferase center (PTC) of M. tuberculosis (2019), Chem. Sci., 10, 8764-8767 .
    View publication on PubMedView publication on EuropePMC

Inhibitors

EC Number Inhibitors Comment Organism Structure
2.3.2.12 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC19595411 Mycobacterium tuberculosis
2.3.2.12 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC19595411 Mycolicibacterium smegmatis
2.3.2.12 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC19595411 Staphylococcus aureus
2.3.2.12 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC22812775 Mycobacterium tuberculosis
2.3.2.12 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC22812775 Mycolicibacterium smegmatis
2.3.2.12 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine i.e. ZINC22812775 Staphylococcus aureus
2.3.2.12 chloramphenicol
-
 Mycolicibacterium smegmatis
2.3.2.12 eperezolid ZINC03813328 Mycobacterium tuberculosis
2.3.2.12 eperezolid ZINC03813328 Mycolicibacterium smegmatis
2.3.2.12 eperezolid ZINC03813328 Staphylococcus aureus
2.3.2.12 linezolid ZINC02008866 Mycobacterium tuberculosis
2.3.2.12 linezolid ZINC02008866 Mycolicibacterium smegmatis
2.3.2.12 linezolid ZINC02008866 Staphylococcus aureus
2.3.2.12 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
2.3.2.12 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
2.3.2.12 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
2.3.2.12 posizolid ZINC03982517 Mycobacterium tuberculosis
2.3.2.12 posizolid ZINC03982517 Mycolicibacterium smegmatis
2.3.2.12 posizolid ZINC03982517 Staphylococcus aureus
2.3.2.12 radezolid ZINC40379938 Mycobacterium tuberculosis
2.3.2.12 radezolid ZINC40379938 Mycolicibacterium smegmatis
2.3.2.12 radezolid ZINC40379938 Staphylococcus aureus
2.3.2.12 sutezolid ZINC03810825 Mycobacterium tuberculosis
2.3.2.12 sutezolid ZINC03810825 Mycolicibacterium smegmatis
2.3.2.12 sutezolid ZINC03810825 Staphylococcus aureus
2.3.2.12 tedizolid ZINC43100953 Mycobacterium tuberculosis
2.3.2.12 tedizolid ZINC43100953 Mycolicibacterium smegmatis
2.3.2.12 tedizolid ZINC43100953 Staphylococcus aureus
2.3.2.12 ZINC19944344
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC19944344 low inhibition Mycolicibacterium smegmatis
2.3.2.12 ZINC19944344
-
 Staphylococcus aureus
2.3.2.12 ZINC35154793
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC35154793
-
 Mycolicibacterium smegmatis
2.3.2.12 ZINC35154793
-
 Staphylococcus aureus
2.3.2.12 ZINC37712815
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC37712815 low inhibition Mycolicibacterium smegmatis
2.3.2.12 ZINC37712815
-
 Staphylococcus aureus
2.3.2.12 ZINC37713642
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC37713642
-
 Mycolicibacterium smegmatis
2.3.2.12 ZINC37713642
-
 Staphylococcus aureus
2.3.2.12 ZINC37715345
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC37715345
-
 Mycolicibacterium smegmatis
2.3.2.12 ZINC37715345
-
 Staphylococcus aureus
2.3.2.12 ZINC54418966
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC54418966
-
 Mycolicibacterium smegmatis
2.3.2.12 ZINC54418966
-
 Staphylococcus aureus
2.3.2.12 ZINC71794395
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC71794395
-
 Mycolicibacterium smegmatis
2.3.2.12 ZINC71794395
-
 Staphylococcus aureus
2.3.2.12 ZINC90290472
-
 Mycobacterium tuberculosis
2.3.2.12 ZINC90290472 low inhibition Mycolicibacterium smegmatis
2.3.2.12 ZINC90290472
-
 Staphylococcus aureus

Localization

EC Number Localization Comment Organism GeneOntology No. Textmining
2.3.2.12 ribosome
-
 Staphylococcus aureus 5840
-
2.3.2.12 ribosome
-
 Mycolicibacterium smegmatis 5840
-
2.3.2.12 ribosome
-
 Mycobacterium tuberculosis 5840
-

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
2.3.2.12 Mg2+ required Mycolicibacterium smegmatis

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Staphylococcus aureus
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycolicibacterium smegmatis
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycobacterium tuberculosis
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycobacterium tuberculosis ATCC 27294
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycolicibacterium smegmatis ATCC 700084
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycobacterium tuberculosis H37Rv
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2 Mycolicibacterium smegmatis mc(2)155
-
 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.3.2.12 Mycobacterium tuberculosis
-
-
-
2.3.2.12 Mycobacterium tuberculosis ATCC 27294
-
-
-
2.3.2.12 Mycobacterium tuberculosis H37Rv
-
-
-
2.3.2.12 Mycolicibacterium smegmatis
-
 i.e. Mycobacterium smegmatis
-
2.3.2.12 Mycolicibacterium smegmatis ATCC 700084
-
 i.e. Mycobacterium smegmatis
-
2.3.2.12 Mycolicibacterium smegmatis mc(2)155
-
 i.e. Mycobacterium smegmatis
-
2.3.2.12 Staphylococcus aureus
-
-
-

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Staphylococcus aureus tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycolicibacterium smegmatis tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycobacterium tuberculosis tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycobacterium tuberculosis ATCC 27294 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycolicibacterium smegmatis ATCC 700084 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycobacterium tuberculosis H37Rv tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?
2.3.2.12 peptidyl-tRNA1 + aminoacyl-tRNA2
-
 Mycolicibacterium smegmatis mc(2)155 tRNA1 + peptidyl(aminoacyl-tRNA2)
-
 ?

Synonyms

EC Number Synonyms Comment Organism
2.3.2.12 MSMEI_5283 locus name Mycolicibacterium smegmatis
2.3.2.12 peptidyl transferase center
-
 Staphylococcus aureus
2.3.2.12 peptidyl transferase center
-
 Mycolicibacterium smegmatis
2.3.2.12 peptidyl transferase center
-
 Mycobacterium tuberculosis
2.3.2.12 PTC
-
 Staphylococcus aureus
2.3.2.12 PTC
-
 Mycolicibacterium smegmatis
2.3.2.12 PTC
-
 Mycobacterium tuberculosis

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.3.2.12 37
-
 assay at Staphylococcus aureus
2.3.2.12 37
-
 assay at Mycolicibacterium smegmatis
2.3.2.12 37
-
 assay at Mycobacterium tuberculosis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
2.3.2.12 7.5
-
 assay at Staphylococcus aureus
2.3.2.12 7.5
-
 assay at Mycolicibacterium smegmatis
2.3.2.12 7.5
-
 assay at Mycobacterium tuberculosis

IC50 Value

EC Number IC50 Value IC50 Value Maximum Comment Organism Inhibitor Structure
2.3.2.12 0.0028
-
 pH 7.5, 37°C Mycolicibacterium smegmatis 1-ethyl-4-[(2-phenylthiazol-4-yl)methyl]piperazine
2.3.2.12 0.0071
-
 pH 7.5, 37°C Mycolicibacterium smegmatis chloramphenicol
2.3.2.12 0.0091
-
 pH 7.5, 37°C Mycolicibacterium smegmatis 1-[(2-methylthiazol-4-yl)methyl]-4-[(2-phenylthiazol-4-yl)methyl]piperazine

General Information

EC Number General Information Comment Organism
2.3.2.12 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
2.3.2.12 evolution the Staphylococcus aureus peptidyl transferase center (PTC) is homologous to Mycobacterium tuberculosis PTC Staphylococcus aureus
2.3.2.12 additional information the enzyme is part of the peptidyl transferase center (PTC) Staphylococcus aureus
2.3.2.12 additional information the enzyme is part of the peptidyl transferase center (PTC) Mycolicibacterium smegmatis
2.3.2.12 additional information the enzyme is part of the peptidyl transferase center (PTC) Mycobacterium tuberculosis