Topic automatically created for discussing the designs at:
https://covid.postera.ai/covid/submissions/KEI-TRE-6cfd789b
| Molecule | Name | Score | Residues |
|  | Famotidine | -32 | HIS(41) ASN(142) GLN(189) |
|  | Ranitidine | -28 | HIS(41) ASN(142) GLU(166) |
|  | Cimetidine | -27 | CYS(44) SER(144) GLU(166) |
|  | Burimamide | -31 | ASN(142) GLU(166) GLN(189) |
The interactions with different residues are not necessarily significant since these molecules are flexible and each of them has several interaction modes (with slightly different scores - best score is saved and reported).
The scores were calculated using the THINK software (https://www.treweren.com) with pharamcophore based docking derived from the protein structure with the PDB code 5RF7.
Hi @EKDavies, Thanks for the submission! Is there any indication from other sources of literature that these compounds would be targeting MPro? Does your docking indicating especially good binding to the protease?
The https://pubmed.ncbi.nlm.nih.gov/8950301/ publication references A S Bourinbaiar and E C Fruhstorfer work on using H2 Antagonists in the treatment of HIV which concludes that the mechanisms was unknown. https://pubmed.ncbi.nlm.nih.gov/8950301/
I suspect the clinical trial was stimulated by Canrong Wu paper (copy at https://treweren.com/papers/Wu_Docking.pdf) which proposes Famotidine as a Mpro inhibitor. If they have validated the potential inhibitors by x-ray or assay then I havent seen the results!
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PS The reason I had used external copies of the 2D image is that uploaded image are not displayed to external visitors to the forum on any of the browsers I have tried! Consequently replacing the img src files has removed the structures!