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Developing Allosteric Inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase
Chayka, Artem ; Danda, Matěj ; Dostálková, Al?běta , et al. ChemMedChem,2024,e202400367. DOI: 10.1002/cmdc.202400367 PubMed ID: 39140451
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Abstract: The use of Fpocket and virtual screening techniques enabled us to identify potential allosteric druggable pockets within the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp). Of the compounds screened, compound 1 was identified as a promising inhibitor, lowering a SARS-CoV-2 RdRp activity to 57% in an enzymatic assay at 10 μM concentration. The structure of compound 1 was subsequently optimized in order to preserve or enhance inhibitory activity. This involved the substitution of problematic ester and aromatic nitro groups with more inert functionalities. The N,N’-diphenylurea scaffold with two NH groups was identified as essential for the compound's activity but also exhibited high toxicity in Calu-3 cells. To address this issue, a scaffold hopping approach was employed to replace the urea core with potentially less toxic urea isosteres. This approach yielded several structural analogues with notable activity, specifically 2,2’-bisimidazol (in compound 55 with residual activity RA = 42%) and (1H-imidazol-2-yl)urea (in compounds 59 and 60, with RA = 50 and 28%, respectively). Despite these advances, toxicity remained a major concern. These compounds represent a promising starting point for further structure-activity relationship studies of allosteric inhibitors of SARS-CoV-2 RdRp, with the goal of reducing their cytotoxicity and improving aqueous solubility.
Purchased from AmBeed: 99-31-0 ; 328-74-5 ; 99-05-8 ; 873-74-5
CAS No. : | 99-31-0 | MDL No. : | MFCD00002522 |
Formula : | C8H7NO4 | Boiling Point : | No data available |
Linear Structure Formula : | - | InChI Key : | KBZFDRWPMZESDI-UHFFFAOYSA-N |
M.W : | 181.15 | Pubchem ID : | 66833 |
Synonyms : |
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Signal Word: | Warning | Class: | |
Precautionary Statements: | P261-P305+P351+P338 | UN#: | |
Hazard Statements: | H315-H319-H335 | Packing Group: | |
GHS Pictogram: |
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