Identification and characterization of new structural scaffolds modulating the activity of Mycobacterium tuberculosis dihydroneopterin aldolase (FolB) in vitro

Falcao, V. C. d. A.; Czeczot, A. d. M.; Alam, M. M.; Park, K.-H. P.; Heo, J.; Woo, M.; Camini, A. M.; Timmers, L. F. S. M.; Shum, D.; Perello, M. A.; Basso, L. A.; Machado, P.; Bizarro, C. V.; Delorme, V. P.

doi:10.1101/2023.11.21.567704

bioRxiv · 10.1101/2023.11.21.567704

Identification and characterization of new structural scaffolds modulating the activity of Mycobacterium tuberculosis dihydroneopterin aldolase (FolB) in vitro

Falcao, V. C. d. A.·Czeczot, A. d. M.·Alam, M. M.·Park, K.-H. P.·Heo, J.·Woo, M.·Camini, A. M.·Timmers, L. F. S. M.·Shum, D.·Perello, M. A.·Basso, L. A.·Machado, P.·Bizarro, C. V.·Delorme, V. P.

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Abstract

Antifolates were among the first broad-spectrum compounds used as antimycobacterial agents and can still be of use when no other therapeutic options are available. The discovery of compounds targeting this essential pathway could lead to new therapeutic agents to treat tuberculosis (TB). In particular, the enzyme required for the conversion of 7,8-dihydroneopterin (DHNP) to 6-hydroxymethyl-7,8-dihydropterin (HP) and glycolaldehyde (GA) in the folate pathway (MtbFolB, a dihydroneopterin aldolase - DHNA, EC 4.1.2.25), has received little attention as a potential drug target. Here, we conducted a small-scale diversity screening to identify MtbFolB inhibitors using a microplate-based enzyme inhibition assay. About 6,000 compounds were assembled for the screening and 19 hits were identified, spanning 5 independent clusters. These compounds were tested in dose-response studies and active compounds selected for kinetic inhibition and time-dependent inhibition studies, leading to compounds with IC50 values ranging from 2.6 to 47 {micro}M. A preliminary structure activity analysis was performed, revealing that bi-sulfonamide compounds could be explored for further optimizations. Docking studies highlighted two modes of binding for pyrazol-3-one compounds and, for the sulfonamide series, indicated several interactions with the catalytic Tyrosine-54 (Tyr54D) and Lysine-99 (Lys99A) residues of MtbFolB. The sulfonamide compound 13 represents the first identified compound directed against MtbFolB with an antimycobacterial activity.

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Falcao, V. C. d. A., Czeczot, A. d. M., Alam, M. M., Park, K.-H. P., Heo, J., Woo, M., Camini, A. M., Timmers, L. F. S. M., Shum, D., Perello, M. A., Basso, L. A., Machado, P., Bizarro, C. V., Delorme, V. P.. 2023-11-21. Identification and characterization of new structural scaffolds modulating the activity of Mycobacterium tuberculosis dihydroneopterin aldolase (FolB) in vitro. https://doi.org/10.1101/2023.11.21.567704

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