Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis

Wang, H.; Xu, M.; Engelhart, C. A.; Zhang, X.; Yan, B.; Pan, M.; Xu, Y.; Fan, S.; Liu, R.; Xu, L.; Hua, L.; Schnappinger, D.; Chen, S.

doi:10.1101/2020.10.27.357681

bioRxiv · 10.1101/2020.10.27.357681

Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis

Wang, H.·Xu, M.·Engelhart, C. A.·Zhang, X.·Yan, B.·Pan, M.·Xu, Y.·Fan, S.·Liu, R.·Xu, L.·Hua, L.·Schnappinger, D.·Chen, S.

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Abstract

Mycobacteria tuberculosis (Mtb) remains the deadliest pathogenic bacteria worldwide. The search for new antibiotics to treat drug-sensitive as well as drug-resistant tuberculosis has become a priority. The essential enzyme phenylalanyl-tRNA synthetase (PheRS) is an antibacterial drug target because of the large differences between bacterial and human PheRS counterparts. In a high-throughput screening of 2148 bioactive compounds, PF-3845, which is a known inhibitor of human fatty acid amide hydrolase (FAAH), was identified inhibiting Mtb PheRS at Ki [~]0.73 {+/-} 0.055 {micro}M. The inhibition mechanism was studied with enzyme kinetics, protein structural modelling and crystallography, in comparison to a PheRS inhibitor of the noted phenyl-thiazolylurea-sulfonamide class. The 2.3-[A] crystal structure of Mtb PheRS in complex with PF-3845 revealed its novel binding mode, in which a trifluoromethyl-pyridinylphenyl group occupies the Phe pocket while a piperidine-piperazine urea group binds into the ATP pocket through an interaction network enforced by a sulfate ion. It represents the first non-nucleoside bi-substrate competitive inhibitor of bacterial PheRS. PF-3845 inhibits the in vitro growth of Mtb H37Rv at [~]24 {micro}M, and the potency of PF-3845 increased against Mtb pheS-FDAS, suggesting on target activity in mycobacterial whole cells. PF-3845 does not inhibit human cytoplasmic or mitochondrial PheRSs in biochemical assay, which can be explained from the crystal structures. Further elaboration of the piperidine-piperazine urea moiety by medicinal chemistry effort will produce potential antibacterial lead with improved selectivity on the cellular level.

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Wang, H., Xu, M., Engelhart, C. A., Zhang, X., Yan, B., Pan, M., Xu, Y., Fan, S., Liu, R., Xu, L., Hua, L., Schnappinger, D., Chen, S.. 2020-10-27. Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis. https://doi.org/10.1101/2020.10.27.357681

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